[gmx-users] virtual sites

[Justin A. Lemkul]

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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================