[gmx-users] User defined Potential Table

Yang Ye leafyoung81-group at yahoo.com
Tue Apr 4 07:02:50 CEST 2006

Hi, Rahul

You need an index file for this purpose. Use make_ndx to generate an 
index file which contains one group including all atoms. Name this group 
as system. Then, you may take down the atom number for those 3-4 
combinations and put them as one group in the index file, while removing 
them from the [ system ]. Name this new group as [ WCA ].

In your mdp file, put following lines

energygrps          =  system WCA
table-extension     =  0
energygrp_table     =  WCA WCA

Then you need to generate the parameter file, name them as 
table_WCA_WCA.xvg. A complete list shall include all combination of the 
group, WCA v.s. system, system v.s. system. But they shall follow the 
standard way, so you may just skip the definition.

For the meaning of the columns inside the table, check manual as well as 
check table#-##.xvg inside the top directory.
This is not a complete tutorial so you may encounter some error 
messages. Just follow the instructions given, you shall be able to do it.

Yang Ye

Rahul Godawat wrote:
> Hi Berk,
> Groamcs user forum has really been extremely useful so far to work 
> with gromacs.  I want to apply a user defined potential for selected 
> energy groups. Its hard to interpret the information on the gromacs 
> webpage and even going through mailing list archives did not answer 
> many questions I have.
> All of my energy groups would interact with normal LJ and use PME for 
> coulombtype (if they have charges) except for 3-4 combinations I want 
> to use WCA potential which has a well defined functional form. How 
> would you suggest going about it.
> Thank you very much
> Rahul
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