[gmx-users] virtual sites

[Gavin Melaugh]

Hi Sikandar

A couple of questions regarding the virtual sites.
1) Do I have to number the virtual site in accordance with the atom
indices of the rest of the molecule?
2) Is the parameters for the virtual site declared in the atomtypes
directive?

Cheers

Gavin

Sikandar Mashayak wrote:
>  in doing so .. by default all pair interactions with virtual sites
> would result in zero forces except those between atoms defined in
> [nonbond_params]
>
> On Thu, May 5, 2011 at 11:57 AM, Sikandar Mashayak
> <symashayak at gmail.com <mailto:symashayak at gmail.com>> wrote:
>
>     hey
>
>     another approach to do this without using energy group exclusion
>     is to define non-bonded interactions parameter explicitly between
>     atoms in ffnonbonded.itp file. You can specify sigma and epsilon
>     to be zero in virtual sites atoms definition and specify
>     individual pair interactions parameters using non-bonded
>     interactions like following ...
>
>     ; virtual site
>     VS1     0        0              0       D       0               0
>     VS2      0        0              0       D       0               0
>     VS3     0        0              0       D       0               0
>
>     [ nonbond_params ]
>     VS1     C     1       1.0             0.25
>     VS2     C     1       1.0             0.25
>     VS2     C     1       1.0             0.25
>
>     --
>     sikandar
>
>     On Thu, May 5, 2011 at 11:47 AM, Gavin Melaugh
>     <gmelaugh01 at qub.ac.uk <mailto:gmelaugh01 at qub.ac.uk>> wrote:
>
>         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.
>
>         Gavin
>
>         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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