[gmx-users] RE: FFGMX

[YOLANDA SMALL]

Hi Junfang,

A small comment about PRODRG....if you want the topology to include hydrogens on
carbons add the line 
ADDHYD C5
(here C5 is the atom number for the carbon that you want a hydrogen added to. 
Read the frequently asked question of PRODRG to find out more about the ADDHYD
and DELHYD options that are available.)

By the way, I usually choose full charges=yes in PRODRG because that is a
necessity with my system.  I cannot really say if this may be the case with
your system.

Hope this helps,
YAS

On Fri, 03 Feb 2006 09:00:35 +1100,  wrote:

> 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
> 
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