[gmx-users] RE: FFGMX

[Junfang.Zhang at csiro.au]

Hi Yang ye and Gromacs users, 


I use Prodrg program to generate topology file for polymers, like
Polyvinylproperlene(PVCap). But Prodrg only targets to GMX force field
instead of OPLS-AA. That means I have to use GMX force field for the
simulation system. In such a system, I also include methane molecules
(CH4). But I cannot find interaction parameters for CH4 in
ffgmxnb.itp/ffgmx.atp. Where can I get the interaction parameters for
CH4?

The topology file produced by Prodrg does not include hydrogen atoms
connected to carbon atoms. So I assume the .pdb file without hydrogen
atoms instead of other pdb files with all hydrogen  or polar hydrgen
should be chosen to match the topology file. Is my understanding
correct?

Before running Prodrg program I have to choose full charges (yes or no).
I noticed the two choices(yes/no) make much difference in the charges
allocated to atoms. Can you please give me some suggestions on how to
make correct choice?



Best regards and thanks,

 

Junfang