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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