CP/MM Tutorial

CP/MM Tutorial 

Jülich, 26/07/2012 

Emiliano Ippoliti: e.ippoliti@grs-sim.de 

Preliminary Information 

To reproduce the calculations in the tutorial and performed the exercises therein you 

need a workstation where to run the required programs that should be already 

installed. To this aim, we will use the main supercomputer of the Aachen 

Rechenzentrum. In order to access this HPC cluster, you need a user account. Each 

student who are already registered in the Aachen TIM-System can activate an account 

on their own through the following procedure: 

• Access your TIM webpage manager: 

https://tim.rz.rwth-aachen.de/enrole/logon 

by inserting your credentials. 

• Click on the “Manage Accounts” icon in the menu at the left of the page. 

• Press the “New” button on the main frame of the page to request the activation 

of a new service. 

• Tick the “Hochleistungsrechnen RWTH Aachen” entry and press “Continue”. 

• Tick the “Ich habe die Nutzungs-/Lizenzbedingungen gelesen und stimme zu” 

and press the “Submit” button. 

In some minutes/hours your account should be created. 

To enter the cluster you can use the ssh command from a terminal window in your 

laptop: 

ssh –Y @cluster.rz.rwth-aachen.de 

For data transfer from and to your laptop use the scp command. 

A very useful user guide for an exhaustive quick start with such a machine can be 

found at the address: 

http://www.rz.rwth-aachen.de/global/show_document.asp?id=aaaaaaaaaacfhzd 

It is strongly suggested to read it and referes to that in case of problem with running 

jobs. 

Introduction 

We want to study the effect of the solvent (water) and the temperature on the dipole 

moment of an acetone molecule. To accomplish that we will resort to several different

software (MOLDEN, CPMD, VMD, Gaussian09, Amber, GROMOS, etc) in order to 

let you taste the everyday working in the biophysical field. 

The procedure can be summarized in the following steps: 

1. Calculate the dipole moment D v of acetone in vacuum 

2. Perform a QM/MM molecular dynamics simulation for the acetone in a 

classical water box at room temperature. 

3. Calculate the dipole moment D for some random snapshots of this simulation 

and take the mean value 

4. Calculate the difference D - D v 

Each file mentioned in this tutorial (in bold) can be found on the Aachen 

supercomputer in the folder: 

/home/ei250498/Tutorials/ACETONE 

under the subfolder whose name starts with the number of the corresponding section 

of this tutorial. 

To do your tests and exercises, work in your own folder in $WORK filesystem by 

creating a folder there by the command: 

Then to go to your folder: 

mkdir $WORK/QMMM_Tutorial 

cd $WORK/QMMM_Tutorial 

1 - Where to start? 

Acetone is the organic compound with the formula (CH3) 2 CO. This colorless, mobile, 

flammable liquid is the simplest example of the ketones: 

Figure 1. Acetone 

To obtain an initial structure we use the MOLDEN program. 1 As for all the programs 

mentioned in this tutorial, the first time in each session you want to use molden you 

need to initialize the environment in order to be able to recall it. This can be done 

with a “source” command: 

source /home/ei250498/PROGRAMS/MODULES/molden.sh 

1 http://www.cmbi.ru.nl/molden/molden.html 

2 An online general guide for the ZMAT Editor can be found at the web address:

Then, you can run molden by simply typing: 

molden & 

In the Molden Control panel at the right, deselect the “Shade” button and press on the 

“ZMAT Editor” button that is a tool to create and/or manipulate structures on screen 

and to optimize the structures on a force field level. 

The use of the editor is rather intuitive. 2 In the following a synthetic list of the steps to 

create the acetone molecule: 

• Press “Add line” 

• Select Carbon from the Periodic Table 

• Press “Substitute atom by Fragment” and without releasing the mouse button 

select the –HC=O 

• Press “Add line” 

• Select Hydrogen from the Periodic Table 

• Click, in the Main screen, on the 4 atoms H,C,O,H in sequence to define the 

connectivity of the new H atom in the molecule 

• Highlight a Hydrogen by pressing on the atom in the Main screen or in the list 

of atoms in Zmat Editor 

• Press “Substitute atom by Fragment” and without releasing the mouse button 

select the –CH3 

• Do the same for the other Hydrogen 

Then, we can save the structure in the xyz format by writing the name of the file in 

the field “File name?”, choosing the “XYZ” format in the menu which appear when 

you press on the square “Cartesian” at the right bottom and finally pressing “Write Z- 

Matrix”. 

Close the ZMAT Editor by clicking the “Close” button on the right top and then by 

pressing on the button with a skull. 

2 - Dipole moment in vacuum 

We will use CPMD to calculate the dipole moment of acetone in gas phase. 

To initialize the environment and be able to use CPMD: 

source /home/ei250498/PROGRAMS/MODULES/cpmd.sh 

Any program can be run interactively on the login node. In the following we report 

the command to do that. However, if your job is supposed to run for more than 5 

minutes this is NOT a good practice: longer jobs should be run on the computational 

node by using the batch system. This can be accomplished by writing a simple batch 

script where you insert the information about your job and then submit the request to 

the batch system through the command: 

2 An online general guide for the ZMAT Editor can be found at the web address: 

http://www.cmbi.ru.nl/molden/zmat/zmat.html#add

sub < 

Some batch script templates called launch_XXX.job can be found in: 

/home/ei250498/TUTORIALS/ACETONE 

If you open them you will found some initial lines starting with #BSUB word that 

represents commands for the batch system: 

#BSUB -J Template 

#BSUB -o output 

#BSUB -e error 

#BSUB -n 2 

#BSUB -W 00:15 

#BSUB -M 700 

#BSUB -a intelmpi 

ß Batch system’s job name 

ß Filename of the batch system’s output messages (and error if no option -e used) 

ß Filename of the batch system’s error messages 

ß Number of cores to be reserve for the job 

ß Hard runtime limit: after the expiration of this time (here 15’) the job will be killed 

ß Set the per-process memory limit in MB 

ß Specify which MPI version you want to use in the parallel run 

followed by some lines which are the commands that the batch system has to run on 

the computational nodes and that are similar to the ones you use in the interactive 

way. 

Refer to the HPC user guide for a more detailed description of all the useful 

commands available for the batch script. 

To check the status of your batched jobs you can use the command: 

bjobs –w 

and to remove a job from the batch list you can use the command: 

bkill 

where the job_id can be read from the list got with the bjobs command. 

A batch script template called launch.job can be found in: 

/home/ei250498/TUTORIALS/ACETONE 

Refer to the HPC user guide to learn how to create a batch script for your jobs. 

To run CPMD with for example 2 cores (everything on the same line): 

mpirun –np 2 cpmd.x /home/ei250498/PROGRAMS/SRC/cpmd/PP 

> & 

/home/ei250498/PROGRAMS/SRC/cpmd/PP is the location where CPMD will look for 

the pseudopotentials files which will be specified in the input file. All the 

pseudopotentials we will use are already present there. 

In order to calculate the dipole moment of the acetone in vacuum we first have to 

optimize the geometry of the molecule we have constructed in the previous step. So,

we need to write an appropriate input file according the syntax of CPMD. 3 By your 

favorite editor, write down the opt_geo.inp text file: 

&INFO 

Acetone molecule 

Geometry optimization 

&END 

&CPMD 

OPTIMIZE GEOMETRY XYZ 

CONVERGENCE ORBITALS 

1.0d-7 

CONVERGENCE GEOMETRY 

7.0d-4 

&END 

&SYSTEM 

ANGSTROM 

SYMMETRY 

ORTHORHOMBIC 

CELL ABSOLUTE 

10.6 10.0 9.8 0.0 0.0 0.0 

CUTOFF 

70. 

&END 

&DFT 

FUNCTIONAL BLYP 

&END 

&ATOMS 

*C_MT_BLYP.psp KLEINMAN-BYLANDER 

LMAX=D 

3 

0.000000 0.000000 0.000000 

1.367073 0.000000 -0.483333 

-0.683537 -1.183920 -0.483333 

*O_MT_BLYP.psp KLEINMAN-BYLANDER 

LMAX=D 

1 

0.000000 0.000000 1.220000 

*H_MT_BLYP.psp KLEINMAN-BYLANDER 

LMAX=P 

6 

1.367073 0.000000 -1.572333 

1.880433 0.889165 -0.120333 

1.880433 -0.889165 -0.120333 

-0.683537 -1.183920 -1.572333 

-0.170177 -2.073085 -0.120333 

-1.710256 -1.183920 -0.120333 

&END 

CPMD Input file 

3 CPMD manual: http://www.cpmd.org/manual.pdf

Any CPMD input file is organized in sections that start with &NAME and end with 

&END. Everything outside those sections is ignored. Also all keywords have to be in 

upper case or else they will be ignored. The sequence of the sections does not matter, 

nor does the order of keywords (except in some special case reported in the manual). 

A minimal input file must have a &CPMD, &SYSTEM, and an &ATOMS section. 

This input file starts with an (optional) &INFO section. This section allows you to put 

comments about the calculation into the input file and they will be repeated in the 

output file. This can be very useful to identify and match your input and output files. 

The first part of &CPMD section instructs the program to do a geometry optimization 

(XYZ suboption specify you want the final structure also in xyz format in a file called 

GEOMETRY.xyz and a ’trajectory’ of the optimization in a file named GEO_OPT.xyz) 

with a tight wavefunction and geometry convergence criterions respectively (default 

10 -5 and 5*10 -4 ). 

The &SYSTEM section contains various parameters related to the simulation cell and 

the representation of the electronic structure. The keywords SYMMETRY, CELL and 

CUTOFF are required and define the (periodic) symmetry, shape, and size of the 

simulation cell, as well as the plane wave energy cutoff (i.e. the size of the basis set), 

respectively. The keyword ANGSTROM specify that the atomic coordinates and the 

supercell parameters and several other parameters are read in Ångströms (pay 

attention: default is atomic units (a.u.) which are always used internally). We define a 

primitive orthorhombic cell with the lattice constants obtained by adding 7 Å in each 

direction to the dimension of the system: the cell has to be large enough to avoid 

significant interactions of the acetone molecule and its electron structure with its 

periodic neighbors. In CPMD all calculations are periodic. Do always a convergence 

test looking for example at the total energy value when you increase the box size! 

The &DFT section is used to select the density functional (FUNCTIONAL) and 

related parameters. In this case we use the gradient corrected BLYP functional 4 (local 

density approximation is the default). 

Finally, the &ATOMS section is needed to specify the atom coordinates and the 

pseudopotential(s), that are used to represent them. The coordinates are taken from 

the structure written by MOLDEN. 

The input for a new atom type is started with a ``*'' in the first column. This line 

further contains the file name where to find the pseudopotential information starting 

in column 2 and several labels as KLEINMAN-BYLANDER, in our case, which specifies 

the method to be used for the calculation of the nonlocal parts of the pseudopotential 

(this method is extremely efficient but also accurate). 

The next line contains information on the nonlocality of the pseudopotential: you can 

specify the maximum l-quantum number with ``LMAX= l '' where l is S, P or D. 5 

On the following lines the coordinates for this atomic species have to be given. 

4 A.D. Becke, J.Chem.Phys. 98 (1993) 5648-‐5652; C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37 

(1988) 785-‐789. 

5 If this is the only input, the program assumes that LMAX is the l for the local 

potential. You can use another local function by specifying ``LOC= ''. In addition it is 

possible to assign the local potential to a further potential with ``SKIP= ''.

The first line gives the number of atoms of the current type. 

--- 

If you start the geometry optimization: 

mpirun -np 2 cpmd.x opt_geo.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP > 

opt_geo.out & 

the calculation should be completed in less than a minute 5 minutes (use 

tail –f opt_geo.out 

to monitor the different steps of the calculation reported in the output file). 

CPMD Output file 

Look at the output file to understand all the information which we can find there. 

At the beginning there is the header where one can see, when the run was started, 

what version of CPMD was used, and when it was compiled: 

PROGRAM CPMD STARTED AT: Tue Jun 1 19:32:59 2010 

SETCNST| USING: CODATA 2006 UNITS 

****** ****** **** **** ****** 

******* ******* ********** ******* 

*** ** *** ** **** ** ** *** 

** ** *** ** ** ** ** ** 

** ******* ** ** ** ** 

*** ****** ** ** ** *** 

******* ** ** ** ******* 

****** ** ** ** ****** 

VERSION 3.13.2 

COMPILED WITH GROMOS-AMBER QM/MM SUPPORT 

COPYRIGHT 

IBM RESEARCH DIVISION 

MPI FESTKOERPERFORSCHUNG STUTTGART 

The CPMD consortium 

Home Page: http://www.cpmd.org 

Mailing List: cpmd-list@cpmd.org 

E-mail: cpmd@cpmd.org 

*** Jan 10 2011 -- 16:03:39 *** 

Then, we find some technical information about the environment (machine, user, 

directory, input file, process id) where this job was run: 

THE INPUT FILE IS: 

opt_geo.inp 

THIS JOB RUNS ON: 

cluster-linux.rz.RWTH-Aachen.DE 

THE CURRENT DIRECTORY IS: 

/home/ei250498/Tutorials/ACETONE/2-CPMD 

THE TEMPORARY DIRECTORY IS: 

/home/ei250498/Tutorials/ACETONE/2-CPMD 

THE PROCESS ID IS: 28735 

Next are the contents of the &INFO section copied to the output:

****************************************************************************** 

* INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO * 

****************************************************************************** 

* Acetone molecule * 

* Geometry optimization * 

****************************************************************************** 

Next section contain a summary of some of the parameters read in from the &CPMD 

section, or their respective default settings; for example the convergence threshold for 

wavefunction optimization (set manually) or the maximum number of iterations 

(default): 

OPTIMIZATION OF IONIC POSITIONS 

PATH TO THE RESTART FILES: ./ 

GRAM-SCHMIDT ORTHOGONALIZATION 

MAXIMUM NUMBER OF STEPS: 

10000 STEPS 

MAXIMUM NUMBER OF ITERATIONS FOR SC: 

10000 STEPS 

PRINT INTERMEDIATE RESULTS EVERY 

10001 STEPS 

STORE INTERMEDIATE RESULTS EVERY 

10001 STEPS 

STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS 

NUMBER OF DISTINCT RESTART FILES: 1 

TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR 

FICTITIOUS ELECTRON MASS: 400.0000 

TIME STEP FOR ELECTRONS: 5.0000 

TIME STEP FOR IONS: 5.0000 

CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-06 

WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS 

THRESHOLD FOR THE WF-HESSIAN IS 0.5000 

MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 10 

STEPS UNTIL DIIS RESET ON POOR PROGRESS: 10 

FULL ELECTRONIC GRADIENT IS USED 

CONVERGENCE CRITERIA FOR GEOMETRY OPTIMIZATION: 3.000000E-04 

GEOMETRY OPTIMIZATION BY GDIIS/BFGS 

SIZE OF GDIIS MATRIX: 5 

GEOMETRY OPTIMIZATION IS SAVED ON FILE GEO_OPT.xyz 

EMPIRICAL INITIAL HESSIAN (DISCO PARAMETRISATION) 

SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS 

NUMBER OF SPLINE POINTS: 5000 

The exchange correlation functionals are reported in the lines coming immediately 

after: 

EXCHANGE CORRELATION FUNCTIONALS 

LDA EXCHANGE: SLATER (ALPHA = 0.66667) 

LDA CORRELATION: 

LEE, YANG & PARR 

[C.L. LEE, W. YANG, AND R.G. PARR, PRB 37 785 (1988)] 

GRADIENT CORRECTED FUNCTIONAL 

DENSITY THRESHOLD: 

1.00000E-08 

EXCHANGE ENERGY 

[A.D. BECKE, PHYS. REV. A 38, 3098 (1988)] 

PARAMETER BETA: 0.004200 

CORRELATION ENERGY 

[LYP: C.L. LEE ET AL. PHYS. REV. B 37, 785 (1988)] 

At this point of the output you find which and how many atoms (and their coordinates 

in a.u.), electrons and states (we are doing a closed shell calculation, so there are only 

doubly occupied states) are in the system, and what pseudopotentials were used with 

which settings: 

*** DETSP| SIZE OF THE PROGRAM IS 3700/ 119392 kBYTES *** 

***************************** ATOMS ****************************

NR TYPE X(bohr) Y(bohr) Z(bohr) MBL 

1 C 0.000000 0.000000 0.000000 3 

2 C 2.583394 0.000000 -0.913367 3 

3 C -1.291698 -2.237285 -0.913367 3 

4 O 0.000000 0.000000 2.305466 3 

5 H 2.583394 0.000000 -2.971279 3 

6 H 3.553503 1.680278 -0.227396 3 

7 H 3.553503 -1.680278 -0.227396 3 

8 H -1.291698 -2.237285 -2.971279 3 

9 H -0.321588 -3.917563 -0.227396 3 

10 H -3.231915 -2.237285 -0.227396 3 

**************************************************************** 

NUMBER OF STATES: 12 

NUMBER OF ELECTRONS: 24.00000 

CHARGE: 0.00000 

ELECTRON TEMPERATURE(KELVIN): 0.00000 

OCCUPATION 

2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 

============================================================ 

| Pseudopotential Report Tue Jan 14 09:55:25 1997 | 

------------------------------------------------------------ 

| Atomic Symbol : C | 

| Atomic Number : 6 | 

| Number of core states : 1 | 

| Number of valence states : 2 | 

| Exchange-Correlation Functional : | 

| Slater exchange : .6667 | 

| LDA correlation : Lee-Yang-Parr | 

| Exchange GC : Becke (1988) | 

| Correlation GC : Lee-Yang-Parr | 

| Electron Configuration : N L Occupation | 

| 1 S 2.0000 | 

| 2 S 2.0000 | 

| 2 P 2.0000 | 

| Full Potential Total Energy -37.702121 | 

| Trouiller-Martins normconserving PP | 

| n l rc energy | 

| 2 S 1.2300 -.49630 | 

| 2 P 1.2300 -.19186 | 

| 3 D .7159 -.19186 | 

| Number of Mesh Points : 615 | 

| Pseudoatom Total Energy -5.370516 | 

============================================================ 

============================================================ 

| Pseudopotential Report Thu Nov 30 13:19:26 1995 | 

------------------------------------------------------------ 

| Atomic Symbol : O | 



| Number of valence states : 2 | 







| 1 S 2.0000 | 

| 2 S 2.0000 | 

| 2 P 4.0000 | 

| Full Potential Total Energy -75.023693 | 



| 2 S 1.0500 -.87404 | 

| 2 P 1.0500 -.33186 | 

| 3 D 1.0500 -.33186 | 


| Pseudoatom Total Energy -15.775323 | 

============================================================ 

============================================================ 

| Pseudopotential Report Thu Nov 30 13:17:19 1995 | 

------------------------------------------------------------ 

| Atomic Symbol : H | 



| Number of valence states : 1 |







| 1 S 1.0000 | 

| Full Potential Total Energy -.462611 | 



| 1 S .5000 -.24002 | 

| 2 P .5000 -.24002 | 


| Pseudoatom Total Energy -.462591 | 

============================================================ 

**************************************************************** 

* ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * 

* C 12.0112 1.2000 NO KLEINMAN S NONLOCAL * 

* P NONLOCAL * 

* D LOCAL * 

* O 15.9994 1.2000 NO KLEINMAN S NONLOCAL * 

* P NONLOCAL * 

* D LOCAL * 

* H 1.0080 1.2000 NO KLEINMAN S NONLOCAL * 

* P LOCAL * 

**************************************************************** 

Then, a section about how the calculation is distributed through the cores: here you 

can understand if something wrong happened and you run for example only a serial 

job! Here below an example of this section by using 8 cores: 

PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA 

NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES 

0 4333 34682 13 246 976 1 1 

1 4335 34684 14 246 976 2 1 

2 4336 34639 13 243 975 1 1 

3 4336 34676 14 244 976 2 1 

4 4334 34682 13 244 976 1 1 

5 4332 34670 14 244 976 2 1 

6 4338 34676 13 244 976 1 1 

7 4342 34680 14 244 976 2 1 

G=0 COMPONENT ON PROCESSOR : 2 

PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA 

*** LOADPA| SIZE OF THE PROGRAM IS 10260/ 120760 kBYTES *** 

OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN 

NUMBER OF CPUS PER TASK 1 

OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN 

*** RGGEN| SIZE OF THE PROGRAM IS 11492/ 121976 kBYTES *** 

The following part of the output we see a summary of the settings read in from the 

&SYSTEM section of the input file or their corresponding defaults and some derived 

parameters (density cutoff, number of plane waves): 

************************** SUPERCELL *************************** 

SYMMETRY: 

ORTHORHOMBIC 

LATTICE CONSTANT(a.u.): 20.03110 

CELL DIMENSION: 20.0311 0.9434 0.9245 0.0000 0.0000 0.0000 

VOLUME(OMEGA IN BOHR^3): 7010.16987 

LATTICE VECTOR A1(BOHR): 20.0311 0.0000 0.0000 



RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0499 0.0000 0.0000 



REAL SPACE MESH: 108 108 100 

WAVEFUNCTION CUTOFF(RYDBERG): 70.00000 

DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000

NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 34686 

NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 277389 

**************************************************************** 

Here we see how CPMD generates the initial guess for the wavefunction 

optimization. In this case it uses a superposition of atomic wavefunctions using an 

(internal) minimal Slater basis: 

*** RINFORCE| SIZE OF THE PROGRAM IS 16052/ 127264 kBYTES *** 

*** FFTPRP| SIZE OF THE PROGRAM IS 19764/ 128656 kBYTES *** 

GENERATE ATOMIC BASIS SET 

C SLATER ORBITALS 

2S ALPHA= 1.6083 OCCUPATION= 2.00 

2P ALPHA= 1.5679 OCCUPATION= 2.00 

O SLATER ORBITALS 


2P ALPHA= 2.2266 OCCUPATION= 4.00 

H SLATER ORBITALS 


INITIALIZATION TIME: 

0.39 SECONDS 

*** GMOPTS| SIZE OF THE PROGRAM IS 24656/ 141780 kBYTES *** 

*** PHFAC| SIZE OF THE PROGRAM IS 24764/ 152468 kBYTES *** 

*** ATOMWF| SIZE OF THE PROGRAM IS 25784/ 154300 kBYTES *** 

ATRHO| CHARGE(R-SPACE): 24.000000 (G-SPACE): 24.000000 

**************************************************************** 

* ATOMIC COORDINATES * 

**************************************************************** 

1 C 0.000000 0.000000 0.000000 

2 C 2.583394 0.000000 -0.913367 

3 C -1.291698 -2.237285 -0.913367 

4 O 0.000000 0.000000 2.305466 

5 H 2.583394 0.000000 -2.971279 

6 H 3.553503 1.680278 -0.227396 

7 H 3.553503 -1.680278 -0.227396 

8 H -1.291698 -2.237285 -2.971279 

9 H -0.321588 -3.917563 -0.227396 

10 H -3.231915 -2.237285 -0.227396 

**************************************************************** 

From the following statement in the output you can see that the Hessian has been 

initialized from a simple guess assuming a molecule with some specified bonds. This 

behavior can be controlled with the keyword HESSIAN. For bulk systems or 

complicated molecules, it may be better to start from a unit Hessian instead: 

INITIALIZE EMPIRICAL HESSIAN 

> 

2 1 3 1 4 1 5 2 6 2 

7 2 8 3 9 3 10 3 

> 

5 1 5 3 6 1 6 4 7 1 

7 3 7 4 8 1 8 2 9 1 

9 2 9 4 10 1 10 4 

TOTAL NUMBER OF MOLECULAR STRUCTURES: 1 

**************************************************************** 

* ATOMIC COORDINATES * 

**************************************************************** 

1 C 0.000000 0.000000 0.000000 

2 C 2.583394 0.000000 -0.913367 

3 C -1.291698 -2.237285 -0.913367 

4 O 0.000000 0.000000 2.305466 

5 H 2.583394 0.000000 -2.971279 

6 H 3.553503 1.680278 -0.227396 

7 H 3.553503 -1.680278 -0.227396 

8 H -1.291698 -2.237285 -2.971279 

9 H -0.321588 -3.917563 -0.227396 

10 H -3.231915 -2.237285 -0.227396

**************************************************************** 

Now the program is ready to start the geometry optimization. You can follow the 

progress of the optimization in the output file: 

CPU TIME FOR INITIALIZATION 

0.81 SECONDS 

================================================================ 

= GEOMETRY OPTIMIZATION = 

================================================================ 

NFI GEMAX CNORM ETOT DETOT TCPU 

EWALD| SUM IN REAL SPACE OVER 

1* 1* 1 CELLS 

1 3.015E-02 4.345E-03 -35.648938 -3.565E+01 0.51 

2 1.889E-02 1.442E-03 -36.307687 -6.587E-01 0.46 

3 1.904E-02 7.725E-04 -36.379166 -7.148E-02 0.46 

… 

26 1.294E-06 1.055E-07 -36.415776 -2.343E-09 0.48 

27 9.933E-07 7.580E-08 -36.415776 -1.233E-09 0.48 

RESTART INFORMATION WRITTEN ON FILE 

./RESTART.1 

ATOM COORDINATES GRADIENTS (-FORCES) 

1 C 0.0000 0.0000 0.0000 -4.443E-02 7.697E-02 -5.004E-02 

2 C 2.5834 0.0000 -0.9134 -3.769E-02 -4.835E-02 4.876E-02 

3 C -1.2917 -2.2373 -0.9134 6.088E-02 8.661E-03 4.903E-02 

4 O 0.0000 0.0000 2.3055 3.158E-02 -5.469E-02 -6.270E-02 

5 H 2.5834 0.0000 -2.9713 -1.090E-02 -5.915E-05 8.858E-03 

6 H 3.5535 1.6803 -0.2274 -9.255E-03 -3.027E-03 -2.712E-04 

7 H 3.5535 -1.6803 -0.2274 6.917E-04 3.287E-03 -1.830E-03 

8 H -1.2917 -2.2373 -2.9713 5.515E-03 9.402E-03 8.862E-03 

9 H -0.3216 -3.9176 -0.2274 -3.189E-03 1.061E-03 -1.824E-03 

10 H -3.2319 -2.2373 -0.2274 7.229E-03 6.496E-03 -2.472E-04 

FILE GEO_OPT.xyz EXISTS, NEW DATA WILL BE APPENDED 

**************************************************************** 

*** TOTAL STEP NR. 27 GEOMETRY STEP NR. 1 *** 

*** GNMAX= 7.696852E-02 ETOT= -36.415776 *** 

*** GNORM= 3.227866E-02 DETOT= 0.000E+00 *** 

*** CNSTR= 0.000000E+00 TCPU= 12.89 *** 

**************************************************************** 

1 2.130E-02 5.311E-03 -35.580799 8.350E-01 0.46 

2 1.574E-02 1.566E-03 -36.324351 -7.436E-01 0.46 

3 5.503E-03 8.729E-04 -36.400043 -7.569E-02 0.46 

... 

A geometry optimization is not much else than repeated wavefunction optimizations, 

where the positions of the atoms are updated according to the forces acting on them. 

In the first part above you can see, the wavefunction optimization. The columns have 

the following meaning: 

• NFI step number (number of finite iterations) 

• GEMAX largest off-diagonal component 

• CNORM average of the off-diagonal components 

• ETOT total energy DETOT change in total energy 

• TCPU time used for this step 

One can see that the calculation stops after the convergence criterion of 1.0d-6 has 

been reached for the GEMAX value. 

After printing the positions and forces of the atoms you see a small report block and 

then another wavefunction optimization starts. The numbers for GNMAX, GNORM, 

and CNSTR stand for the largest absolute component of the force on any atom,

average force on the atoms, and the largest absolute component of a constraint force 

on the atoms respectively. They allow you to monitor the progress of the convergence 

of the geometry optimization. 

Finally, at the end of the geometry optimization, you can see that the forces and the 

total energy have decreased from their initial values as it is to be expected: 

**************************************************************** 

*** TOTAL STEP NR. 3737 GEOMETRY STEP NR. 214 *** 

*** GNMAX= 2.827646E-04 [3.64E-02] ETOT= -36.489908 *** 

*** GNORM= 1.395703E-04 DETOT= -1.769E-05 *** 

*** CNSTR= 0.000000E+00 TCPU= 9.63 *** 

**************************************************************** 

================================================================ 

= END OF GEOMETRY OPTIMIZATION = 

================================================================ 

and we have the final summary of the results; the atom coordinates and a breakdown 

of the total energy into the various components: 


./RESTART.1 

**************************************************************** 

* * 

* FINAL RESULTS * 

* * 

**************************************************************** 

ATOM COORDINATES GRADIENTS (-FORCES) 

1 C 0.3033 -0.3710 0.4996 2.238E-04 -3.750E-05 -1.867E-04 

2 C 2.8157 0.1207 -0.8206 -2.828E-04 1.186E-04 1.534E-04 

3 C -1.4005 -2.3884 -0.6592 -1.866E-05 -5.129E-05 1.748E-04 

4 O -0.3055 0.7755 2.4178 1.488E-05 -9.553E-05 2.593E-04 

5 H 2.5171 0.5750 -2.8280 7.045E-06 -1.029E-04 -2.289E-04 

6 H 3.8187 1.6721 0.1124 -6.949E-05 1.507E-04 -3.226E-05 

7 H 3.9948 -1.5943 -0.7676 1.188E-04 -1.722E-05 1.350E-04 

8 H -1.5584 -2.1576 -2.7186 1.045E-05 -8.026E-05 -1.718E-04 

9 H -0.5710 -4.2692 -0.3267 -5.208E-05 -4.544E-05 5.413E-05 

10 H -3.2775 -2.3193 0.2103 -1.609E-04 1.615E-04 -2.245E-04 

**************************************************************** 

ELECTRONIC GRADIENT: 

MAX. COMPONENT = 8.03517E-07 NORM = 6.81662E-08 

NUCLEAR GRADIENT: 

MAX. COMPONENT = 2.82765E-04 NORM = 1.39570E-04 

TOTAL INTEGRATED ELECTRONIC DENSITY 

IN G-SPACE = 24.000000 

IN R-SPACE = 24.000000 

(K+E1+L+N+X) TOTAL ENERGY = -36.48990756 A.U. 

(K) KINETIC ENERGY = 27.70023623 A.U. 

(E1=A-S+R) ELECTROSTATIC ENERGY = -27.60801450 A.U. 

(S) ESELF = 29.92067103 A.U. 

(R) ESR = 1.71581582 A.U. 

(L) LOCAL PSEUDOPOTENTIAL ENERGY = -27.66180959 A.U. 

(N) N-L PSEUDOPOTENTIAL ENERGY = 1.82151808 A.U. 

(X) EXCHANGE-CORRELATION ENERGY = -10.74183777 A.U. 

GRADIENT CORRECTION ENERGY = 

-0.58344734 A.U. 

**************************************************************** 

The last section of the output reports the memory allocation and the timing of the run: 

================================================================ 

BIG MEMORY ALLOCATIONS 

SCR 785159 CATOM 190652

PME 520040 PSI 330270 

YF 330270 GNL 240960 

ATWFR 301200 SCR 785149 

XF 330270 RHOE 165135 

---------------------------------------------------------------- 

[PEAK NUMBER 99] PEAK MEMORY 4872541 = 39.0 MBytes 

================================================================ 

**************************************************************** 

* * 

* TIMING * 

* * 

**************************************************************** 

SUBROUTINE CALLS CPU TIME ELAPSED TIME 

INVFFTN 44858 3172.00 323.62 

FFT-G/S 269168 2733.40 274.36 

FWFFT 18690 1730.00 175.40 

I NVFFT 14953 1726.20 173.92 

GCENER 3738 1265.70 128.33 

FWFFTN 22436 1242.70 125.49 

FFTCOM 33643 817.30 127.30 

VPSI 3747 593.00 58.45 

GRADEN 3738 460.30 47.00 

RHOOFR 3737 448.90 45.11 

N-FFTCOM 67294 389.10 84.91 

ODIIS 3737 381.20 38.66 

XCENER 3738 353.30 35.86 

FNONLOC 3747 233.70 23.72 

PHASE 33643 219.10 22.22 

VOFRHOA 3738 172.50 17.50 

VOFRHOB 3738 131.30 12.75 

EICALC 3738 94.90 9.90 

RNLSM1 3747 66.90 6.84 

RGS 3950 38.60 3.57 

RNLSM2 664 35.50 3.48 

---------------------------------------------------------------- 

TOTAL TIME 16305.60 1738.41 

**************************************************************** 

CPU TIME : 4 HOURS 33 MINUTES 47.00 SECONDS 

ELAPSED TIME : 0 HOURS 30 MINUTES 10.50 SECONDS 

*** CPMD| SIZE OF THE PROGRAM IS 41068/ 152348 kBYTES *** 

PROGRAM CPMD ENDED AT: Tue Jan 10 20:03:09 2011 

================================================================ 

= COMMUNICATION TASK AVERAGE MESSAGE LENGTH NUMBER OF CALLS = 

= SEND/RECEIVE 43407. BYTES 36127. = 

= BROADCAST 321. BYTES 15557. = 

= GLOBAL SUMMATION 360. BYTES 79725. = 

= GLOBAL MULTIPLICATION 0. BYTES 1. = 

= ALL TO ALL COMM 876851. BYTES 100937. = 

= PERFORMANCE TOTAL TIME = 

= SEND/RECEIVE 5675.900 MB/S 0.276 SEC = 

= BROADCAST 94.488 MB/S 0.053 SEC = 

= GLOBAL SUMMATION 8.258 MB/S 10.435 SEC = 

= GLOBAL MULTIPLICATION 0.000 MB/S 0.001 SEC = 

= ALL TO ALL COMM 417.428 MB/S 212.029 SEC = 

= SYNCHRONISATION 0.025 SEC = 

================================================================ 

If you look in your directory, you will see the following files: 

Name 

GEOMETRY 

GEOMETRY.xyz 

GEO_OPT.xyz 

HESSIAN 

LATEST 

Content 

Final ionic positions and velocities (in a.u.) 

Final ionic positions and velocities in xyz format 

All the ionic positions along the geometry optimization 

Approximate Hessian used in geometry optimization 

Info on the last restart file: filename and # times written

RESTART.1 

Restart binary file from which it is possible restart a new 

calculation 

Now we want to calculate the dipole of the acetone in the “zero temperature” 

optimized structure just found by using the RESTART.1 file to retrieve the information. 

We can do that modifying the input file this way (see dipole.inp file): 


PROPERTIES 

RESTART WAVEFUNCTION COORDINATES LATEST 

&END 

&PROP 

DIPOLE MOMENT 

&END 

… 

PROPERTIES keyword tells CPMD to look at the section &PROP where it is specifies 

which properties it has to calculate. 

RESTART keyword tells CPMD to read WAVEFUNCTION and COORDINATES from the 

restart file written in the LATEST file (which was generated in the previous 

calculation). 

The rest of the input file is the same of the previous one: the coordinates will be not 

read (since are taken from the restart file) but some number as to put anyway to avoid 

the program stops writing some error! 

Run the job: 

mpirun -np 2 cpmd.x dipole.inp //home/ei250498/PROGRAMS/SRC/cpmd/PP / 

> dipole.out & 

In the output file you can see that the following new section: 

CALCULATE DIPOLE MOMENT 

**************************************************************** 

* PROPERTY CALCULATIONS * 

**************************************************************** 

RV30| WARNING! NO WAVEFUNCTION VELOCITIES 

RESTART INFORMATION READ ON FILE 

./RESTART.1 


CENTER OF INTEGRATION (CORE CHARGE): 0.37726 -0.65932 0.02482 

DIPOLE MOMENT 

X Y Z TOTAL 

0.35426 -0.61017 -0.98996 1.21566 atomic units 

0.90044 -1.55090 -2.51623 3.08990 Debye 

3 – The electrostatic grid

The next step will be to create a box with an acetone molecule and several water 

molecules. We will use for that the xleap program belonging to the Amber11 6 

molecular dynamics package. This package has been devised to deal with biological 

systems (aminoacids, nucleic acids, etc) and so our acetone has not recognized by it. 

This is also the case when we want to study some drug which interacts with 

“traditional” biological systems. 

In particular, xleap do not know how to assign the partial charges to each atom of 

acetone. To do that we will use a standard procedure which has been directly 

suggested by the developers of the Amber force fields and which they use to tune that 

parameters which is not possible to determine experimentally. The procedure is based 

on calculating at quantum level the electrostatic potential on a grid around the 

molecule and then to determine the so-called RESP charges to assign at each atom in 

order to reproduce the electrostatic field. 

According the recipe of Amber developers we will use the Gaussian09 package 7 to 

calculate the electrostatic grid by using the 6-31G(d,p) localized basis set and B3LYP 

exchange correlation functional. 

First, we need to optimize the geometry again: the level of theory are different and in 

principle the optimized structures could be different! Here it is the input file 

opt_geom.com for Gaussian: 

%NProcShared=2 

%chk=./opt_geom.chk 

%mem=600MB 

#p opt b3lyp/6-31G(d,p) nosymm iop(6/7=3) gfinput 

Acetone geometry optimization 

0 1 

C 0.000000 0.000000 0.000000 

O 0.000000 0.000000 1.220000 

C 1.367073 0.000000 -0.483333 

C -0.683537 -1.183920 -0.483333 

H 1.367073 0.000000 -1.572333 

H 1.880433 0.889165 -0.120333 

H 1.880433 -0.889165 -0.120333 

H -0.683537 -1.183920 -1.572333 

H -0.170177 -2.073085 -0.120333 

H -1.710256 -1.183920 -0.120333 

Note: Remember to leave two blank line at the end of the file (do not ask me why J) 

Run the optimization: 

1. Initialize the environment (this time we use the module command since the 

program was installed by the staff of the cluster and not by us): 

2. Run Gaussian: 

module load CHEMISTRY 

module load gaussian09 

6 You can find the manual at the web address: http://ambermd.org/doc11/ 

7 Gaussian09 online manual: http://www.gaussian.com/g_tech/g_ur/g09help.htm

g09 opt_geom.com & 

3. After about one minute the job will end and you can check that the 

optimization has been successfully this way: 

grep -B 1 Maximum opt_geom.log 

Use Molden to retrieve the coordinates of the last optimized configuration: 

molden opt_geom.log & 

in the Molden Control panel press the “Geom. conv.” button and the Geom 

Convergence windows will appear. In that windows you can select any step of the 

optimization procedure; select the last one and save the structure. 

Now, use Gaussian again to calculate the electrostatic grid by the 

electrostatic_grid.com input file: 

%NProcShared=8 

%chk=./electrostatic_grid.chk 

%mem=600MB 

#p b3lyp/6-31G(d,p) nosymm iop(6/33=2) pop(chelpg,regular) guess=read gfinput 

Acetone electrostatic grid calculation 

0 1 

C 0.1066280 -0.1846610 0.1346160 

O -0.3060700 0.5300980 1.0273310 

C 1.4973060 -0.0081640 -0.4519990 

C -0.7415970 -1.3007560 -0.4520680 

H 1.4366050 0.1927160 -1.5279620 ß Optimized coordinates 

H 2.0063930 0.8173940 0.0467940 

H 2.0826090 -0.9274690 -0.3338980 

H -0.8854310 -1.1476190 -1.5280030 

H -0.2379310 -2.2672580 -0.3343160 

H -1.7110070 -1.3291270 0.0468420 

The electrostatic grid will be written in the log file: look for the string “ESP fit Center”. 

4 – Partial charges 

The program Antechamber inside the Amber10 and Amber11 package 8 is able to read 

the electrostatic grid in a log file of Gaussian and calculate the RESP charges associated 

to the atoms of your molecule. To use Antechamber and every other program of the 

Amber11 suite, we firstly need to initialize the environment: 

source /home/ei250498/PROGRAMS/MODULES/amber11.sh 

8 The current version (07-‐2012) of Antechamber in Amber12 is buggy. Do not use Amber12 for 

these calculations.

Copy the log file of Gaussian with the electrostatic grid information on a new directory 

and use the following command: 9 

antechamber -i electrostatic_grid.log -fi gout -c resp -nc 0 -m 1 -o 

acetone.resp.prep -fo prepi -rn ACET 

Actually, Antechamber recalls several programs in sequence that produce many 

different intermediate files in your directory. When the process ends correctly you 

should see the file acetone.resp.prep that is the file with the partial RESP charges that 

we will use in the next step (copy it in a new directory and move to it). 

5 – Water box 

It is time to create the water box containing the acetone and the files necessary to run a 

short classical Molecular Dynamics (MD) run. In fact, we want then to perform a 

classical pre-equilibration of the system, in order to relax it near to a “stable state”. 10 

For this aim we will use the Graphical User Interface Xleap of Amber11: 

xleap -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB & 

where the file leaprc.ff99SB is used to load all libraries which contains the parameters of 

the Amber force field 99SB. Such a force field like any others has been tuned to 

describe aminoacids, nucleic acids, etc but there is no information about acetone. For 

this reason we have calculated the partial charges, which now we can load in Xleap by 

typing the following command (in the Xleap main window): 11 

loadamberprep acetone.resp.prep 

and for the same reason some other parameters are still missing and have to be added 

manually. Most of them can be retrieved by the “general Amber force field for organic 

molecules GAFF”: 

loadamberparams $AMBERHOME/dat/leap/parm/gaff.dat 

other ones, however, have to provide manually. It is not difficult to calculate them but 

here we will no explain how to do 12 . We have already prepared a file with such missing 

parameters (above all bond and angles ones) and they can be load in Xleap by the 

following command: 

loadamberparams /home/ei250498/TUTORIALS/ACETONE/5-XLEAP/acetone.frcmod 

You can now give a look at your system by the command edit: 

9 Run simply the command “antechamber” to have a short description of the meaning of all the 

option recognized by antechamber. 

10 Remember the time step for a classical MD run is ~ps, while the time step for a quantum MD is 

~fs. So, the classical pre-‐equilibration is essential since typical relaxation times are of the order 

of 10s-‐100s of ps! 

11 The syntax for any Xleap command can be recall by typing the command without any 

arguments. 

12 Refer to the Amber manual, for example.

edit ACET 

You can also check if all the parameters for the acetone have been loaded: 

check ACET 

Finally, you can save the topology and coordinates files for your ACET unit by typing: 

saveamberparm ACET acetone.top acetone.rst 

However, we want to study the acetone in water and therefore we need to solvate the 

system, before: 

solvatebox ACET TIP3PBOX 14 

TIP3PBOX specifies that we solvate with the classical water model molecule 

“TIP3P” 13 ; an orthorhombic box whose walls are at least 14 Å from any acetone’s atoms 

has been created: 

edit ACET 

From the new window you can also look at the partial charges and other parameters of 

your system: 

• Select the atoms 

• Edit/Edit selected atoms 

Finally, we save the topology and coordinates files for our solvated system: 

saveamberparm ACET acetone_solv.top acetone_solv.rst 

Copy the two files to another folder. 

By the VMD software 14 you can visualize your system: 

source /home/ei250498/PROGRAMS/MODULES/vmd.sh 

vmd –parm7 acetone_solv.top –rst7 acetone_solv.rst 

VMD is also installed on your laptop. You can transfer the files needed to VMD on 

your laptop and use them locally: this strategy could be worth in the cases your network 

connection was really slow. 

6 – Pre Equilibration 

13 http://en.wikipedia.org/wiki/Water_model 

14 VMD User’s Guide: http://www.ks.uiuc.edu/Research/vmd/current/ug/

We need now to equilibrate the system at force field level in order to later start the 

QM/MM simulation from a configuration “not so far” from an equilibrium one (at the 

QM/MM level). 

To run MD simulation we will use the “sander” program of the AMBER11 package. 

We proceed this way: 15 

1. First, classical minimization of the system restraining the acetone molecule to 

the initial position: this step is performed since the initial Xleap solvation is not 

physically reasonable (no hydrogen bonds, etc) and this way we favour water 

molecules to orient correctly around the acetone: 

mpirun -np 2 sander.MPI -O -i 1-restraint.inp -o eq_restraint.out –c 

acetone_solv.rst -p acetone_solv.top -r eq_restraint.rst –ref 

acetone_solv.rst -inf eq_restraint.info & 

Note: the command “tail eq_restraint.info” can be used to monitor the minimization and 

verify that it does not reach the max number of steps but stop before satisfying the 

convergence criteria. 

2. Then, a not constrained minimization is performed: 

mpirun -np 2 sander.MPI -O -i 2-minimization.inp –o 

eq_minimization.out -c eq_restraint.rst -p acetone_solv.top -r 

eq_minimization.rst -inf eq_minimization.info & 

3. Now, we take the system at 300 K with MD at constant volume and a linear 

heating. In this step we constrain weakly acetone to the initial position so that 

water can spread all around the acetone without forming “holes”. Since the liquid 

water relaxation time is order of 10 ps we need to perform a > 10 ps MD: 

mpirun -np 2 sander.MPI -O -i 3-heating.inp -p acetone_solv.top -c 

eq_minimization.rst -ref eq_minimization.rst -o eq_heating.out -r 

eq_heating.rst -x eq_heating.crd -e eq_heating.en -inf 

eq_heating.info & 

4. Finally, we couple our system simultaneously to a thermostat at 300 K and a 

barostat at 1 atm and perform an NPT simulation to let the density of the system 

to reach the equilibrium value at room condition (~ 1g/cm 3 since the most is 

formed by water): 

mpirun -np 2 sander.MPI -O -i 4-eq_density.inp -p 

acetone_solv.top -c eq_heating.rst -o eq_density.out -r 

eq_density.rst -x eq_density.crd -e eq_density.en –inf 

eq_density.info & 

Note: when the last step has ended, you can fast analyze the behavior of all the 

physically relevant quantities of your system (like the density for example) by using 

the perl script “process_mdout.perl”: 

15 All the input file for sander can be found in the folder: 

/home/ei250498/TUTORIALS/ACETONE/6-SANDER

Box Density 

• mkdir analysis 

• cd analysis 

• process_mdout.perl ../eq_density.out 

• xmgrace summary.DENSITY 

Why is density smaller than 1g/cm 3 ? 

7 – Reimaging 

Let’s give a look at the last configuration you obtained from the classical molecular 

dynamics equilibration: 

cd .. 

vmd -parm7 acetone_solv.top -rst7 eq_density.rst 

What did happen to our orthorhombic box? 

The image shows your system without applying the periodic boundary conditions 

(PBC) that sander and all the other programs of Amber11 use. So, molecules drift 

over time and may span multiple periodic cells; this is normal when you are working 

on Amber11 or on some other molecular dynamics package. However, now we want 

to move to CPMD in order to perform a QM/MM MD simulation, and CPMD does 

not apply “automatically” PBC. Consequently, we need to “reimage” the coordinates 

into the primary unit cell. We can use the “ptraj” program 16 of the Amber11 suite to 

accomplish this task. Move the topology and coordinates files to another folder and 

then create the input file eq_density.ptraj for ptraj: 

16 http://ambermd.org/doc10/AmberTools.pdf

trajin eq_density.rst 

ß coordinates file to read 

trajout eq_density_reimaged.rst restart ß output file in the same format as the input 

center :1 ß center the box to the geometric center of residue 1 

image center 

ß force all the molecules into the primary unit cell 

Run ptraj according this syntax: 

ptraj acetone_solv.top < eq_density.ptraj 

Verify that the imaging has been correctly done: 

vmd -parm7 acetone_solv.top -rst7 eq_density_reimaged.rst.1 

8 – Convert MD files 

Copy the topology and the “reimaged” coordinates files to a new directory and typing 

the following command: 

source /home/ei250498/PROGRAMS/MODULES/conv_7.sh 

Conv_7.x acetone_solv.top eq_density_reimaged.rst.1 solvate 

Conv_7.x is an in-house program written some years ago to convert the Amber MD 

files in the GROMOS format. This because the QM/MM interface of CPMD works 

with such a format. The option “solvate” let us specify that the water molecules 

should be treated as solvent ones: this is useful only if you are interested to read in the 

log files of CPMD energies and other quantities partitioned in solute and solvent 

components. 

If you get an error like this: 

PGFIO-F-231/formatted read/unit=12/error on data conversion. 

File name = acetone_solv.top formatted, sequential access 

record = 2538 

In source file Conv.f, at line number 280 

is because you are using an Amber version later of 2010. As of the end of 2010, xleap 

writes in the topology files two short sections:

%FLAG SCEE_SCALE_FACTOR 

and 

%FLAG SCNB_SCALE_FACTOR 

introduced to allow you to set the scaling coefficients for individual elements. These 

sections are not understood by our converter and should be removed from our 

topology file before processing it with Conv7.x. This can be simply done by opening 

the topology file with a text editor: 

vi acetone_solv.top 

This procedure can also be done automatically by using the perl script Conv7.pl in 

place of Conv7.x 

Conv_7.pl acetone_solv.top eq_density_reimaged.rst.1 solvate 

The presence of these two sections is completely negligible for our aims, including 

performing classical molecular dynamics. 

The converter will produce 5 files: 

• gromos.top the Gromos topology file for our system 

• gromos.inp the Gromos input file 

• gromos.g96 the coordinates file in g96 format 

• gromacs.top the Gromacs topology file 

• ffgro96.itp the itp file for the Gromacs software 

We need only the first 3 files, but some changes 17 have to be done in order to 

correctly set up a QM/MM MD simulation: 

Changes in gromos.inp 

1 - In the section SYSTEM the two numbers should be in sequence: 

Number of (identical) solute (not necessarily the QM part!) molecules 

Number of (identical) solvent (not necessarily the MM part!) molecules 

Such information can be retrieved, for example, by typing on the prompt 

command line: 

2 - In the section BOUNDARY: 

tail gromacs.top 

The first number should be 0 for isolated system; >0 if PBC in parallelepiped 

box has been used;

gromos.g96 file. 

90.0 is the angle between the x and z axis of the box. 

The last number is ignored by CPMD in QM/MM simulations. 

3 - In the section SUBMOLECULES the numbers in sequence should be: 

Number of (different) solute molecules. 

Index of the last atom of the first solute molecule. 

Index of the last atom of the second solute molecule. 

... 

Such data can be read from the file gromos.g96: 

vi gromos.g96 

4 - In the section PRINT you could want to modify the first number which give 

you the number of steps after that CPMD write info of the energy in the output 

file (20 is usually enough). 

5 - In the section FORCE, under the line of 1's (which turns the various force 

components on), we have to put: 

The number of different layers, usually 2 (Solute and solvent) 

Index of the last atom of layer 1 

Index of the last atom of layer 2 

... 

Changes in gromos.top 

In the section ATOMTYPENAME replace the names of the types of the atoms, 

from the standard generic force field library "gaff": 

to the Amber force field library: 

vi $AMBERHOME/dat/leap/parm/gaff.dat 

vi $AMBERHOME/dat/leap/parm/parm99.dat 

The correctly modified files gromos_mod.top and gromos_mod.inp can be found in: 

/home/ei250498/TUTORIALS/ACETONE/8-Conv_7 

9 – QM/MM MD 

Copy the modified files and the grooms.g96 file to a new directory. 

At this point, we have all the files which describe the MM part and its interactions; 

the last step will be to write the input file for CPMD with the instructions for the 

simulation and the definition of the QM part. A CPMD input file for a QM/MM

simulation is similar to the CPMD input file for a standard QM calculation which has 

been described in paragraph 2 (section &INFO, &CPMD, &SYSTEM, &ATOMS, 

&DFT). However, there are 6 main differences which should always be taken into 

account when you deal with the QM/MM interface of CPMD: 

1. In the &CPMD section the keyword QMMM has to be added. 

2. A new &QMMM section, which we will explain in detail below, is 

mandatory. 

3. The QM atoms are specified in the &ATOMS section similar to normal 

CPMD calculations. Instead of explicit coordinates one has to provide the 

atom index as given in the Gromos topology and coordinates files: 

vi gromos.g96 

4. The keyword ANGSTROM in the &SYSTEM section cannot be used, so any 

length has to be specified in a.u. 

5. The option ABSOLUTE in the keyword CELL cannot be used. Therefore, the 

correct syntax for the size of the rectangular box AxBxC is 

A B/A C/A 0 0 0 

6. The QM system in a QM/MM calculation can only be dealt as isolated system, 

i.e. without explicit PBC since there is the MM environment all round it. 

Even though we are requesting an isolated system calculation (SYMMETRY 

keyword with the option ISOLATED SYSTEM or 0), the calculation is, in fact, 

still done in a periodic cell (we are still using plane wave basis set!). Since 

acetone has a dipole moment, we have to take care of the long range 

interactions between periodic images and there are methods (activated with 

the keyword POISSON SOLVER in the &SYSTEM section) implemented in 

CPMD to compensate for this effect. We will choose the TUCKERMAN Poisson 

solver 18 since it has been proven to be the most effective one with typical 

systems studied in biology. Decoupling of the electrostatic images in the 

Poisson solver requires to increase the box size over the dimension of the 

molecule: practical experience shows that 3.5 Å space between the outmost 

atoms and the box is usually sufficient for typical biological systems. 

&QMMM section 

In this paragraph we will review the most relevant keywords to specify in the 

&QMMM section of the CPMD input file. See for example 19 for a complete 

list: 

TOPOLOGY: On the next line the name of a Gromos topology file 

has to be given. 

COORDINATES: On the next line the name of a Gromos96 format 

coordinate file has to be given. 

INPUT: On the next line the name of a Gromos input file has to 

be given. 

18 G.J. Martyna and M. E. Tuckerman, J. Chem. Phys. 110, 2810 (1999). 

19 http://www.cpmd.org/manual/node258.html

AMBER: 

ELECTROSTATIC 

COUPLING: 

An Amber functional form for the classical force field 

is used. 

The electrostatic interaction of the quantum system 

with the classical system is explicitly kept into account 

for all classical atoms at a distance r ≤ RCUT_NN from 

any quantum atom and for all the MM atoms at a 

distance of RCUT_NN < r ≤ RCUT_MIX and a charge 

larger than 0.1e (NN atoms). MM-atoms with a charge 

smaller than 0.1e and a distance of RCUT_NN < r ≤ 

RCUT_MIX and all MM-atoms with RCUT_MIX < r ≤ 

RCUT_ESP are coupled to the QM system by a ESP 

coupling Hamiltonian (EC atoms). 

If the additional LONG RANGE keyword is specified, the 

interaction of the QM-system with the rest of the 

classical atoms is explicitly kept into account via 

interacting with a multipole expansion for the QMsystem 

up to quadrupolar order. A file named 

MULTIPOLE is produced. 

If LONG RANGE is omitted the quantum system is 

coupled to the classical atoms not in the NN-area and 

in the EC-area list via the force-field charges. 

If the keyword ELECTROSTATIC COUPLING is omitted, 

all classical atoms are coupled to the quantum system 

by the force-field charges (mechanical coupling): 

computational expensive calculation! 

RCUT_NN: 

RCUT_MIX: 

RCUT_EXP: 

UPDATE LIST: 

SAMPLE 

INTERACTING: 

ARRAYSIZES: 

The cutoff distance for atoms in the nearest neighbor 

region from the QM-system is read from the next line. 

We will use the default value of 10 a.u. 

The cutoff distance for atoms in the intermediate 

region is read from the next line. We will use the value 

of 15 a.u. 

The cutoff distance for atoms in the ESP-area is read 

from the next line. We will use the value of 20 a.u. 

On the next line the number of MD steps between 

updates of the various lists of atoms for 

ELECTROSTATIC COUPLING is given. At every list 

update a file INTERACTING_NEW.pdb is created (and 

overwritten). 

The sampling rate for writing a trajectory of the 

interacting subsystem is read from the next line. With 

the additional keyword OFF or a sampling rate of 0, 

those trajectories are not written. 

Parameters for the dimensions of various internal arrays 

can be given in this block. The syntax is one label and

the according dimension per line. The suitable 

parameters can be estimated using the script 

estimate_gromos_size.sh: 

estimate_gromos_size.sh gromos_mod.top 

This section of the input has to be terminated by a line 

containing END ARRAYSIZES. 

Now, we have all the elements to write a CPMD input file for a QM/MM simulation. 

But which steps do we need to perform a stable Car-Parrinello MD? 

We have the equilibrated coordinates at room conditions obtained from a classical MD: 

this is a good starting point, however we still need to equilibrate the system at QM/MM 

level since the two levels of theory are different. 

Therefore, as we have done in the second paragraph, we should firstly optimize the 

geometry of the system. Unfortunately, all the optimizer algorithms in CPMD do not 

work together the QM/MM interface. Consequently, we have to use some “trick” to find 

a minimal energy structure (at QM/MM level). In particular in this tutorial we will 

perform a simulated annealing (keyword ANNEALING IONS), i.e. we run a CP-dynamics 

where and gradually removing kinetic energy from the nuclei by multiplying velocities 

with a factor (in our case it is set to 0.99, so 1% of the kinetic energy will be removed in 

every step). Here it is the annealing.inp file which perform this preliminary step: 

&QMMM 

TOPOLOGY 

gromos_mod.top 

COORDINATES 

gromos.g96 

INPUT 

gromos_mod.inp 

ELECTROSTATIC COUPLING LONG RANGE 

RCUT_NN 

10 

RCUT_MIX 

15 

RCUT_ESP 

20 

UPDATE LIST 

100 

SAMPLE_INTERACTING 

0 

AMBER 

ARRAYSIZES 

MAXATT 16 

MAXAA2 11 

MAXNRP 20 

MAXNBT 15 

MAXBNH 16 

MAXBON 13 

MAXTTY 14 

MXQHEH 22 

MAXTH 13 

MAXQTY 10 

MAXHIH 10 

MAXQHI 10 

MAXPTY 14 

MXPHIH 28 

MAXPHI 11 

MAXCAG 11 

MAXAEX 20024 

MXEX14 22

END ARRAYSIZES 

&END 


QMMM 

MOLECULAR DYNAMICS CP 

ISOLATED MOLECULE 

QUENCH BO 

ANNEALING IONS 

0.99 

TEMPERATURE 

300 

EMASS 

600. 

TIMESTEP 

5.0 

MAXSTEP 

10000 

TRAJECTORY SAMPLE 

0 

STORE 

100 

RESTFILE 

1 

&END 

&SYSTEM 

POISSON SOLVER TUCKERMAN 

SYMMETRY 

0 

CELL 

18.61 1.11 0.95 0 0 0 

CUTOFF 

70. 

CHARGE 

0.0 

&END 

&DFT 

FUNCTIONAL BLYP 

&END 

&ATOMS 

*H_MT_BLYP.psp KLEINMAN-BYLANDER 

LMAX=S 

6 

4 5 6 8 9 10 

*C_MT_BLYP.psp KLEINMAN-BYLANDER 

LMAX=P 

3 

2 3 7 

*O_MT_BLYP.psp KLEINMAN-BYLANDER 

LMAX=P 

1 

1 

&END 

Some comments on the keywords in the &CPMD section which are not explained, yet: 

MOLECULAR DYNAMICS CP: 

ISOLATED MOLECULE: 

QUENCH BO: 

Perform a molecular dynamics run. 

CP stands for a Car-Parrinello type of MD. 

Calculate the ionic temperature assuming that 

the system consists of an isolated molecule or 

cluster. 

the wavefunction is converged at the 

beginning of the MD run.

TEMPERATURE: 

EMASS: 

TIMESTEP: 

MAXSTEP: 

TRAJECTORY SAMPLE: 

STORE: 

RESTFILE: 

The initial temperature for the atoms in Kelvin 

is read from the next line: we start from 300 K 

since it is the temperature at which we 

equilibrate the system classically. 

The fictitious electron mass in atomic units for 

the CP dynamics is read from the next line. 

We choose 600 a.u. but ideally a careful set of 

tests should be done to verify that adiabaticity 

conditions to be met 20 : this and the following 

one are the only parameters to tune in order to 

decouple the electronic and ionic degrees of 

freedom and minimize their energy transfer. 

The time step in atomic units is read from the 

next line. We use the default time step of 5 a.u. 

~ 0.12 fs. 

The maximum number of steps for molecular 

dynamics to be performed. The value is read 

from the next line. 

Store the atomic positions, velocities and 

optionally forces at N every time step on the 

TRAJECTORY file. N is read from the next line. 

If N=0 the trajectory file will not be written. 

The RESTART file is updated every N steps. N 

is read from the next line. Default is at the end 

of the run. 

The number of distinct RESTART files 

generated during CPMD runs is read from the 

next line. The restart files are written in turn. 

Default is 1. 

Moreover, here it is a simple procedure to obtain the sizes of the box to insert under the 

CELL keyword by using standard bash commands: 

• Create a file with the coordinate of the atoms belong to the QM part: 

grep CET gromos.g96 > QM.coor 

• Reorder the lines in the column 5 (6,7) for the coordinate x (y,z) with an 

increasing numerical (-n) order: 

sort -k 5 -n QM.coor 

• Take the last value (L) of the column (in nm), subtract it to the first (F) one, 

add 0.7 nm (i.e. 2 * 3.5 Å for the Poisson solver’s requirements) and then 

convert it to a.u.: 

echo "(L - F + 0.7)*10/0.529" | bc –l 

20 http://www.theochem.ruhr-‐uni-‐bochum.de/research/marx/marx.pdf

• Finally remember that under the CELL keyword of the CPMD input file the 

size of the quantum cell will be inserted according to the syntax: 

size_x size_y/size_x size_z/size_x 0 0 0 

1 - ANNEALING 

We are now ready to run the annealing (copy all the file in a folder called 

ANNEALING): 

mpirun -np 2 cpmd.x annealing.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP 

> annealing.out & 

While the simulation proceeds you can monitor the decreasing temperature (third 

column named TEMPP) this way: 

tail -f annealing.out 

When the temperature reaches about 2-4 K we can “softly” stop the calculation (that 

is in order to make it write a RESTART file) by typing on the prompt line: 

touch EXIT 

The final configuration will be stored in the RESTART.1 file. 

More files will be generated during a QM/MM CP simulation: 

QMMM_ORDER 

CRD_INI.g96 

CRD_FIN.g96 

INTERACTING.pdb 

INTERACTING_NEW.pdb 

The first line specifies the total number of atoms (NAT) and the 

number of quantum atoms (NATQ). The subsequent NAT lines 

contain, for every atom, the gromos atom number, the internal 

CPMD atom number, the CP species number isp and the 

number in the list of atoms for this species NA(isp). The 

quantum atoms are specified in the first NATQ lines. 

Contains the positions of all atoms in the first frame of the 

simulation in Gromos extended format (g96). 

Contains the positions of all atoms in the last frame of the 

simulation in Gromos extended format (g96). 

Contains (in a non-standard PDB-like format) all the QM atoms 

and all the MM atoms in the electrostatic coupling NN list. The 

5-th column in this file specifies the gromos atom number as 

defined in the topology file and in the coordinates file. The 10- 

th column specifies the CPMD atom number as in the 

TRAJECTORY file. The quantum atoms are labeled by the 

residue name QUA. 

The same as before, but it is created if the file 

INTERACTING.pdb is detected in the current working 

directory of the CPMD run.

MM_CELL_TRANS 

ENERGIES 

The QM system (atoms and wavefunction) is always recentered 

in the given supercell. This file contains, the 

trajectory of the re-centering offset for the QM-box. The first 

column ist the frame number (NFI) followed by the x-, y-, and 

z-component of the cell-shift vector. 

Contains all the energies along the trajectory. 

Let’s give a closer look at the output file annealing.out which present some new 

sections: 

CAR-PARRINELLO MOLECULAR DYNAMICS 

PATH TO THE RESTART FILES: ./ 

ITERATIVE ORTHOGONALIZATION 

MAXIT: 30 

EPS: 

1.00E-06 

MAXIMUM NUMBER OF STEPS: 

10000 STEPS 

MAXIMUM NUMBER OF ITERATIONS FOR SC: 

10000 STEPS 

PRINT INTERMEDIATE RESULTS EVERY 

10001 STEPS 

STORE INTERMEDIATE RESULTS EVERY 

100 STEPS 

STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS 

NUMBER OF DISTINCT RESTART FILES: 1 

TEMPERATURE IS CALCULATED ASSUMING AN ISOLATED MOLECULE 

In CPMD, atoms are frequently referred to as ions, which may be confusing. This is 

due to the pseudopotential approach, where you integrate the core electrons into the 

(pseudo)atom which then could be also described as an ion. See for example the 

following output segment: 

FICTITIOUS ELECTRON MASS: 600.0000 

TIME STEP FOR ELECTRONS: 5.0000 

TIME STEP FOR IONS: 5.0000 

QUENCH SYSTEM TO THE BORN-OPPENHEIMER SURFACE 

SIMULATED ANNEALING OF IONS WITH ANNERI = 0.990000 

ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED 

ION DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED 

This part of the output tells us, that the TIMESTEP keyword was recognized as well as 

the output option and that there will be no temperature control, i.e. we will do a 

microcanonical (NVE-ensemble) simulation. 

Then, several sections devoted to describe in detail the QM/MM interface and its data 

immediately follow: 

INITIALIZATION TIME: 

1.05 SECONDS 

*** MDPT| SIZE OF THE PROGRAM IS 95528/ 288728 kBYTES *** 


*** ATOMWF| SIZE OF THE PROGRAM IS 98100/ 302796 kBYTES *** 

ATRHO| CHARGE(R-SPACE): 24.000000 (G-SPACE): 24.000000 

RE-CENTERING QM SYSTEM AT EVERY TIME STEP 

BOX TOLERANCE [a.u.] 7.00000000000000 

BOX SIZE [a.u.] 

QM SYSTEM SIZE [a.u.] 

X DIRECTION: CELLDIM = 18.6100; XMAX-XMIN= 5.3773 

Y DIRECTION: CELLDIM = 20.6571; YMAX-YMIN= 7.3868 

Z DIRECTION: CELLDIM = 17.6795; ZMAX-ZMIN= 4.3595 

>>>>>>>> QUENCH SYSTEM TO THE BORN-OPPENHEIMER SURFACE

!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!! 

THE QM SYSTEM DOES NOT HAVE AN INTEGER CHARGE. 

A COMPENSATING CHARGE OF 0.000040 HAS BEEN 

DISTRIBUTED OVER THE NN ATOMS. 

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 

… 

0.000040 e of charge to compensate: for all practical purposes this is zero! 

After the force initialization section finally the MD begins: 

NFI EKINC TEMPP EKS ECLASSIC EHAM EQM DIS TCPU 

1 0.00006 297.0 -54.34715 -51.01094 -51.01088 -36.46342 0.218E-04 1.53 

2 0.00056 293.9 -54.34671 -51.04477 -51.04421 -36.46309 0.863E-04 1.54 

3 0.00136 290.9 -54.34661 -51.07860 -51.07724 -36.46309 0.191E-03 1.52 

4 0.00201 287.9 -54.34663 -51.11193 -51.10992 -36.46319 0.335E-03 1.52 

... 

The individual columns have the following meaning: 

NFI 

EKINC 

TEMPP 

EKS 

ECLASSIC 

EHAM 

EQM 

DIS 

TCPU 

Step number (number of finite iterations) 

Fictitious kinetic energy of the electronic degrees of freedom 

Temperature (= kinetic energy / degrees of freedom) for atoms 

(ions) 

Kohn-Sham energy; equivalent to the potential energy in 

classical MD 

The total energy in a classical MD, but not the conserved 

quantity for CP-dynamics (ECLASSIC = EHAM - EKINC). 

Energy of the total CP-Hamiltonian; the conserved quantity. 

Energy of QM part (electrons + nuclei contribution) 

Mean squared displacement of the atoms from the initial 

coordinates. 

Time needed for this step 

Finally we get a summary of some averages and root mean squared deviations for 

some of the monitored quantities. This is quite useful to detect unwanted energy drifts 

or too large fluctuations in the simulation: 


./RESTART.1 

**************************************************************** 

* AVERAGED QUANTITIES * 

**************************************************************** 

MEAN VALUE +/- RMS DEVIATION 

[-^2]**(1/2) 

ELECTRON KINETIC ENERGY 0.000867 0.300539E-03 

IONIC TEMPERATURE 37.2640 52.8318 

DENSITY FUNCTIONAL ENERGY -56.788301 0.907159 

CLASSICAL ENERGY -56.369667 1.48329 

CONSERVED ENERGY -56.368800 1.48357 

NOSE ENERGY ELECTRONS 0.000000 0.00000

NOSE ENERGY IONS 0.000000 0.00000 

CONSTRAINTS ENERGY 0.000000 0.00000 

RESTRAINTS ENERGY 0.000000 0.00000 

ION DISPLACEMENT 0.306287 0.932230E-01 

CPU TIME 1.5641 

2 – TEST 

To verify that the reached configuration is physically "reasonable", a good test is to 

run a simulation in a NVE ensemble and monitoring the temperature (column 3) and 

the physical energy (column 5): if after some steps these two quantities stabilize 

(usually oscillating around a value of temperature smaller than 100 K) then we can be 

confident that the RESTART.1 file previously obtained is a good minimal energy 

structure. On the other hand, if energy and/or temperature continuously increase that 

means we have not a good structure and another annealing procedure is required by 

starting from another point (for example after heating the system at 300 K in order to 

move the system away from that “wrong” energy potential basin). The test can be 

accomplished by the following procedure: 

• Create a new folder: 

mkdir TEST 

cd TEST 

• Copy the following files from the previous calculation: 

cp ../gromos* . 

cp ../RESTART.1 RESTART 

cp ../annealing.inp 

test.inp 

• Modify the test.inp file in order to change the &CPMD section so as to 

appear: 


RESTART COORDINATES VELOCITIES WAVEFUNCTION 


MOLECULAR DYNAMICS CP 

ISOLATED MOLECULE 

EMASS 

600. 

TIMESTEP 

5.0 

MAXSTEP 

3000 

TRAJECTORY SAMPLE 

0 

&END 

Note: in the RESTART line there is no LATEST option: this way CPMD expects 

to read data from a file named exactly “RESTART”. 

• Run the test:

mpirun -np 8 cpmd.x test.inp 

/home/ei250498/PROGRAMS/SRC/cpmd/PP > test.out & 

• Monitor the simulation: 

tail –f test.out 

• When it ends you can plot on a graph the temperature and the physical energy 

by gnuplot: 

gnuplot 

p 'ENERGIES' u 1:3 w l 

p 'ENERGIES' u 1:5 w l 

quit 

3 – HEATING 

If the test went well, we can come back to the configuration obtained by annealing 

and start heating the system to room temperature. There are several methods 

implemented in CPMD to do that. We choose to increase the target temperature of a 

thermostat (coupled to the system) linearly at each step by performing a usual CP 

dynamics. A simple Berendsen-type thermostat 21 will be applied. 

Two more keywords are required in &CPMD section with respect the previous input 

file: 

1. TEMPERATURE with the option RAMP; 3 numbers has to be specified on the line 

below the keyword: initial and target temperature in K and the ramping speed 

in K per atomic time unit (to get the change per timestep you have to multiply 

it with the value of TIMESTEP). Read the initial temperature from the output 

file of the annealing procedure. 

2. BERENDSEN with the option IONS; 2 numbers has to be specified on the line 

below the keyword: the target temperature (the initial one in our case) and the 

time constant τ in a.u. (0.12 ps is a reasonable value). 

The procedure to accomplish the heating can be summarized this way: 

• Create a new folder: 

mkdir HEATING 

21 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, J. R. Haak 

J. Chem. Phys, 81, 3684 (1984).

cd HEATING 

• Copy the following files from the previous calculation: 

cp ../ANNEALING/gromos* . 

cp ../ANNEALING/RESTART.1 RESTART 

cp ../TEST/test.inp 

heating.inp 

• Modify heating.inp according the rules above mentioned: 

vi heating.inp 

by adding the two following lines in the &CPMD section: 

• Monitor the temperature: 

BERENDEN IONS 

3.8 5000 

TEMPERATURE RAMP 

3.8 340.0 1 

tail –f heating.out 

• If the temperature reach approximately the target temperature even before the 

MAXSTEP number of steps are performed you can stops the simulation: 

touch EXIT 

4 – PRODUCTION RUN 

We are finally ready to run a CP molecular dynamics in room conditions. 

To do that, as usual, we will create a new folder: 

mkdir PRODUCTION-RUN 

cd PRODUCTION-RUN 

and then we will copy the necessary files there in order to start the calculation from 

the last configuration got from the heating procedure: 

cp ../HEATING/gromos* . 

cp ../HEATING/RESTART.1 RESTART 

cp ../HEATING/heating.inp 

cpmd.inp 

To run CP molecular dynamics we need to modify the previous input file: 

• We want to restart from previous wavefunction, coordinates and velocities 

since we want to conserve the temperature information from the RESTART file.

Therefore we will preserve the option VELOCITIES in the RESTART keyword 

and we will remove TEMPERATURE keyword. 

We will replace the Berendsen thermostat with the Nose-Hoover chains 22 : this 

because the second kind of thermostat preserves the Maxwell distribution of 

the velocities and so it is more physically meaningful. In more technical 

words, it provides an NVT ensemble for a system in equilibrium. 

The keyword that turns it on is NOSE, and then you have to specify the degrees 

of freedom to which you want to apply it (IONS); the target temperature in 

Kelvin and the thermostat frequency in cm-1 are read from the next line: 

NOSE IONS 

300 4000 

For the choice of frequency at which the energy transfer happens, you have 

only to pay attention not to select a resonance vibrational frequency of your 

system. 

• We will reintroduce the keyword MAXSTEP to perform 10000 steps (or more if 

you have time: typical CPMD trajectories nowadays are tens of ps long!) 

• Finally, we want to save 10 restart files (i.e. configurations from which we 

will calculate the dipole moment of acetone) equally separated in time along 

the trajectory. We can do that by properly using the keyword RESTFILE and 

STORE: 

STORE 

100 

RESTFILE 

10 

This way CPMD will create ten restart files in sequence called RESTART.1, 

RESTART.2, …, RESTART.10 each one after 1000 steps of dynamics. 

Running meaningful Car-Parrinello dynamics simulation requires adiabaticity 

conditions to be met, i.e. the separation of the electronic and ionic degrees of 

freedom. 

Theoretically such separation can be achieved by separating the power spectrum of 

the orbital classical fields from the phonon spectrum of the ions (the gap between the 

lowest electronic frequency and the highest ionic frequency should be large enough). 

Since the electronic frequencies depend on the fictitious electron mass EMASS one 

should carefully optimize its value and rise the lowest frequency appropriately. 

The adiabaticity can be observed by running test simulations and looking at the 

energy components. 

In particular, the fictitious kinetic energy of the electronic degrees of freedom (EKINC, 

second column in the ENERGIES file) might have a tendency to grow. However, after 

an initial transfer of a little kinetic energy, the electrons should be much “colder" than 

the ions, since only then will the electronic structure remain close to the Born- 

Oppenheimer surface and thus the wavefunction and forces derived from it will be 

22 S. Nosé and M. L. Klein, Mol. Phys. 50, 1055 (1983); S. Nosé, Mol. Phys. 52, 255 (1984); S. Nosé, 

J. Chem. Phys. 81, 511 (1984); S. Nosé, Prog. Theor. Phys. Suppl. 103, 1 (1991); W. G. Hoover, 

Phys. Rev. A 31, 1695 (1985).

meaningful. Therefore, we must always monitor the behavior of the EKINC in order 

to verify the system keeps being in the adiabatic regime: 

TOTAL INTEGRATED ELECTRONIC DENSITY 

IN G-SPACE = 24.000000 

IN R-SPACE = 24.000000 

(K+E1+L+N+X+Q+M) TOTAL ENERGY = -57.87866446 A.U. 

(K+E1+L+N+X) TOTAL QM ENERGY = -36.47942711 A.U. 

(Q) TOTAL QM/MM ENERGY = 0.00000000 A.U. 

(M) TOTAL MM ENERGY = -21.38112962 A.U. 

DIFFERENCE = -0.01810773 A.U. 

(K) KINETIC ENERGY = 27.71754549 A.U. 

(E1=A-S+R) ELECTROSTATIC ENERGY = -27.62122216 A.U. 

(S) ESELF = 29.92067103 A.U. 

(R) ESR = 1.68558813 A.U. 

(L) LOCAL PSEUDOPOTENTIAL ENERGY = -29.41090607 A.U. 

(N) N-L PSEUDOPOTENTIAL ENERGY = 3.57237860 A.U. 

(X) EXCHANGE-CORRELATION ENERGY = -10.73722297 A.U. 

GRADIENT CORRECTION ENERGY = 

-0.58313547 A.U. 

NFI EKINC TEMPP EKS ECLASSIC EHAM EQM DIS TCPU 

1 0.00001 302.5 -57.87866 -54.48084 -54.48082 -36.47943 0.538E-05 1.50 

2 0.00011 302.3 -57.87721 -54.48093 -54.48082 -36.47936 0.214E-04 1.47 

3 0.00027 302.2 -57.87578 -54.48109 -54.48082 -36.47937 0.480E-04 1.35 

4 0.00037 302.0 -57.87431 -54.48118 -54.48081 -36.47937 0.849E-04 1.50 

5 0.00039 301.9 -57.87280 -54.48119 -54.48080 -36.47937 0.132E-03 1.35 

6 0.00039 301.8 -57.87125 -54.48118 -54.48079 -36.47937 0.190E-03 1.35 

7 0.00037 301.6 -57.86966 -54.48116 -54.48078 -36.47937 0.258E-03 1.67 

8 0.00037 301.5 -57.86803 -54.48115 -54.48078 -36.47936 0.336E-03 1.35 

9 0.00037 301.3 -57.86636 -54.48114 -54.48077 -36.47936 0.425E-03 1.46 

NBPML: 80733 ELEMENTS IN THE PAIRLIST 

10 0.00037 301.2 -57.86466 -54.48114 -54.48077 -36.47935 0.523E-03 1.37 

11 0.00036 301.0 -57.86291 -54.48113 -54.48077 -36.47934 0.632E-03 1.46 

12 0.00035 300.9 -57.86112 -54.48111 -54.48076 -36.47932 0.752E-03 1.35 

13 0.00035 300.7 -57.85927 -54.48107 -54.48073 -36.47931 0.881E-03 1.35 

14 0.00034 300.5 -57.85740 -54.48106 -54.48072 -36.47929 0.102E-02 1.46 

15 0.00033 300.4 -57.85551 -54.48106 -54.48073 -36.47928 0.117E-02 1.35 

16 0.00032 300.2 -57.85357 -54.48105 -54.48073 -36.47927 0.133E-02 1.46 

17 0.00031 300.0 -57.85159 -54.48103 -54.48072 -36.47926 0.150E-02 1.35 

18 0.00030 299.8 -57.84956 -54.48101 -54.48070 -36.47925 0.169E-02 1.51 

19 0.00030 299.7 -57.84751 -54.48099 -54.48070 -36.47924 0.188E-02 1.42 

Ensuring adiabaticity of CP dynamics consists of decoupling the two subsystems and 

thus minimizing the energy transfer from ionic degrees of freedom to electronic ones. 

In this sense the system during CP dynamics simulation should be kept in a 

metastable state. 

Hint: any time you notice something strange (and even if you do not!) I very 

useful suggestion is ALWAYS look at your simulations by some visualization tool: 

the most of the problem are immediately identified at a glance… 

To visualize a CP-‐MM simulation you can use vmd: 23 

23 Any command of vmd can be also execute by the GUI of the program: refer to its manual for 

details.

vmd -g96 CRD_INI.g96 -cpmd TRAJECTORY 

5 – DIPOLE CALCULATION 

As a last step we want to calculate the dipole moment for each snapshot saved in 

ten restarts file previously collected and then make the mean value in order to 

give this way an estimate of the temperature and entropic effects due to the 

environment formed by the solvent. 

Create a new folder and copy the restart files and the other needed files in this 

directory: 

mkdir DIPOLE_CALCULATION 

cp ../ PRODUCTION-RUN/RESTART.* . 

cp ../ PRODUCTION-RUN/gromos* . 

cp ../ PRODUCTION-RUN/cpmd.inp dipole.in 

cp ../PRODUCTION-RUN/LATEST . 

and modify the input file to calculate the dipole moment as you have learnt in the 

second paragraph: 

… 



RESTART WAVEFUNCTION COORDINATES LATEST 

PROPERTIES 

RESTFILE 

0 

&END 

&PROP 

DIPOLE MOMENT 

&END 

… 

The keyword LATEST is inserted in order to perform the ten calculations in a 

comfortable way: in fact, if you want CPMD read the RESTART.X file you only need 

to replace that name in the first line of the file LATEST. The keyword RESTFILE 

with value 0 guarantees that CPMD does not write a RESTART file at the end of 

each calculation (we do not need it, now), so avoiding it overwrites the ones we 

have copied from the PRODUCTION-‐RUN folder. 

So, you can perform the following sequence of very fast calculations (less than 3 

sec!), being careful to modify the name in the first line of the file LATEST each 

time:

mpirun -np 2 cpmd.x dipole.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP > 

dipole1.out & 


dipole2.out & 


dipole3.out & 


dipole4.out & 


dipole5.out & 


dipole6.out & 


dipole7.out & 


dipole8.out & 


dipole9.out & 


dipole10.out & 

Note: you could have skipped this procedure by using the keyword 

DIPOLE DYNAMICS SAMPLE 

1000 

in the previous CP calculation. Such a keyword makes CPMD save the 

coordinates of the dipole moments every 1000 steps on a file called DIPOLE. An 

example is saved in the folder: 

/home/ei250498/TUTORIALS/ACETONE/9-CPMD-MM/4-PRODUCTION-RUN/DIPOLE/ 

However, these values are polarizations (in a.u.): they have to be multiply by the 

volume to obtain the correct values of the dipole in a.u. 

At this point you have only to extract each value of the dipole moment: 

grep -B 1 -A 4 "X 

grep -B 1 -A 4 "X 

Y" dipole1.out 

Y" dipole2.out 

… 

and calculate the arithmetic mean D. 

What is the difference with respect the value in vacuum we calculate in the 

second paragraph?

What is the qualitative reason of such a difference? 

The solvent effect can be separated in two different components: the 

geometry variation of the solute with respect to the gas phase (temperature 

effect), and the different polarization of the wavefunction. 

How could you proceed if you wanted to identify the contribution of the two 

parts?

CP/MM Tutorial

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