CP/MM Tutorial

%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;