Molecular Modeling Introduction - University at Buffalo

Marek
Freindorf
Molecular Modeling
Introduction
University at Buffallo
January 2008

Introduction (www.ccr.buffalo.edu)
Marek
Freindorf
mfrein@buffalo.edu

Introduction, time frame and organization
One class a week:
- 4 weeks, I course - QM
- 4 weeks, II course - MM
- 4 weeks, III course - QM/MM
Each class has:
- 30 min electronic lecture (by me)
- 120 min individual work (a shorter task)
with a computer
During each section:
- a computer project (a longer task)
After each section:
- a seminar (oral presentation)
Grade:
- 50% participation in classes, 50% presentations

Communication
SSH secure shell
Server
Desktop
Software for visualization
- DS Viewer
- DS Visualizer (www.accelrys.com)
Software for
calculations
- Q-Chem
- AMBER

Hardware
Dell Linux Cluster:
- 1000 nodes, 2-processors
3.2 GHz Intel Xeon
2 Gb, 4 Gb and 8 Gb
- Operating System: Linux
Disk Storage:
- 35 Tb scratch space

Windows
Ceating a directory

Windows
Ceating a directory

Windows
Ceating a directory

Windows
Ceating a directory

SSH Environment
SSH is a secure environment, used
for communication between a client
window (a local desctop) and a
server (a supercomputer)
Creating a profile
Just your name

SSH Environment
Editing a profile
Server address
My user name

SSH Environment
Login into my account on a server
Password

SSH Environment
Command line

SSH Environment
File transfer

SSH Environment
Local desktop
Server

SSH Environment
Transfering a file from a local
desctop into a server
Headlight a file, and press a
mouse right click

SSH Environment
Transfering a file from a server
into a local desctop
Headlight a file, and
press a mouse right click

UNIX System
Showing a name of a current
directory:
> pwd

UNIX System
Making a new directory:
> mkdir dirname

UNIX System
Changing a directory:
> cd dirname

UNIX System
Changing back a directory:
> cd ..

UNIX System
Listing a directory:
> ls dirname

UNIX System
Removing a directory (must be empty):
> rmdir dirname

UNIX System
Copying a file:
> cp oldname newname

UNIX System
Copying a file into another directory:
> cp name.ext /another/directory

UNIX System
Copying a file into another directory:
> cp /another/directory/filname .

UNIX System
Copying a file into another directory:
> mv name.ext /another/directory

UNIX System
Removing a file:
> rm filname

UNIX System
Editing a file:
> vi filename

UNIX System
Edition mode of vi -
press "Esc" to go into edition mode
press "i" to go into insert mode
press ":" to go into command mode
> x - deleting a character
> dd - deleting a line
> dw - deleting a word

UNIX System
Insert mode of vi -
press "i" to go into insert mode
press "Esc" to go into edition mode
press ":" to go into command mode
> type and use "Enter" to
go to the next line

UNIX System
Command mode of vi -
press ":" to go into command mode
press "Esc" to go into edition mode
press "i" to go into insert mode
> :w! filename - saving a file
> :q! - quiting vi

UNIX System
Finding a character:
(edition mode)
> /character
a keyboard "slash"

UNIX System
Marking a part of the text:
(edition mode)
> mchart1
Go to a line which is a
beginning of the text
and type ma

UNIX System
Marking a part of the text:
(edition mode)
> mchart2
Go to a line which is
an ending of the text
and type mb

UNIX System
Saving a marked text:
(command mode)
>'a,'b w marked.txt
The marked text will be
saved in a file in your
current directory

UNIX System
Moving through a text:
(edition mode)
> ^f - moving forward
> ^b - moving backward
a keyboard control
> 1G - go to the beginning
> G - go to the end

UNIX System
Substituting a text:
(command mode)
> :1,$ s/oldchar/newchar/g
from the beginning
to the end of the
text
subsitute

Simple QM geometry optimization of water
Initial geometry of the water
molecule is taken from the
DS Viewer program

Simple QM geometry optimization of water
The initial
geometry of
thw molecule
should be
saved in a
PDB format

Simple QM geometry optimization of water
Uploading the
water PDB file
into the server

Simple QM geometry optimization of water
Copy and paste the
water coordinates from
the PDB file into a
q-chem input file

Simple QM geometry optimization of water
Preparing the PBS file,
which runs q-chem
calculations of the
water molecule

Simple QM geometry optimization of water
Submitting a job for
execution

Simple QM geometry optimization of water
Results of the
calculations are in the
"water.out" file

Simple QM geometry optimization of water
The end of the
"water.out" file, after
geometry
optimization

Simple QM geometry optimization of water
Transforming output
coordinates into a PDB file

Simple QM geometry optimization of water
Downloading the optimized
coordinated from the server into the
local desctop

Simple QM geometry optimization of water
Visualizing the
structure
using the
DS Viewer
program

Seminar
A Title of My Presentation
My name, and affiliation

Seminar
Presentation Schedule:
- Introduction
- Computational details
- Results of the calculations
- Conclusions
- Future work

Seminar
Technical tips of the presentation
- Use large fonts (18-36pt)
- All numbers should have units
- All tables should have column descriptions
- All figures should have axis descriptions
- Use different colors to headlight important
results

Seminar
Technical tips of the presentation
- Prepare 1 slide per 1-2 minutes talk
- Show how your calculations are different from
calculations done by others
- Show comparison of the calculated results
with availabe experimental data
- Try to explain results of the calculations,
do not show just numbers

Seminar
Technical tips of the presentation
- Less is More !