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