[gmx-users] virtual sites

Gavin Melaugh gmelaugh01 at qub.ac.uk
Thu May 5 18:47:18 CEST 2011

Hi Justin

I do not intend to have charges on the sites. All I want is;
when a CH3 group gets close to the site it feels a repulsive force. I
have calculated a sigma and epsilon value for this interaction.


Justin A. Lemkul wrote:
> 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

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