[gmx-users] virtual sites

Justin A. Lemkul jalemkul at vt.edu
Thu May 5 18:28:20 CEST 2011

Gavin Melaugh wrote:
> Hi Justin
> I am reading the manual at the moment. I want to include some virtual
> sites in my molecule so that only surrounding CH3s atom type C3 interact
> with then. All other atoms I don't want to interact with them. Do I
> create energy groups in the index file called say "virtual sites" and
> "exclusions", and list all the indices of the atom types that I don't
> want to interact with the virtual site in one group and all the virtual
> sites in another.
> e.g
> [virtual sites]
> 17 18 19 20
> [virtsite_exclus]
> 1 2 3 4 5 6 7 8 9 .....

In a general sense, yes, that's the right approach.  Note that if any of these 
sites is charged and/or you're using PME, then this whole exclusion thing goes 
out the window, as has been discussed several times in recent days.  Using 
energygrp_excl applies only to short-range nonbonded interactions.  If you need 
complete exclusion, you may have to look into tabulated potentials if this is 
the case.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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