[gmx-users] virtual sites

[Sikandar Mashayak]

 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>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>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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>
>
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