[gmx-users] virtual sites set up for topology file

[Gavin Melaugh]

Hi

I am trying to alter a topology to include 3 virtual sites and I have a
few queries, the answers to which are not obvious form the manual.
Do I declare the virtual sites in the atomtypes directive like so

;type     mass           charge      ptype     sigma(nm)    
epsilon(kjmol-1)
   CB     12.011000      0.000000       A      0.355000      0.292880
   CA     12.011000     -0.115000       A      0.355000      0.292880
   VS1     0.0                        0.0            V     
0.0           0.0
   VS2     0.0                        0.0            V     
0.0           0.0
   VS3     0.0                        0.0            V     
0.0           0.0

Do I give them an index number in the atoms directive e.g.

[atoms]
; atomnr  type   resnr  residue   name    cgnr     charge     mass
    1      CA       1   CGE        CA       1     -0.1150     12.0110
    2      CB       1   CGE        CB       1      0.0000     12.0110
    3      CA       1   CGE        CA       2     -0.1150     12.0110
    4      CB       1   CGE        CB       2      0.0000     12.0110
    5      CA       1   CGE        CA       3     -0.1150     12.0110
     ..........
     ..........
  229      VS1      2   VIR        VS1     85      0.0000      0.0000
  230      VS2      3   VIR        VS2     86      0.0000      0.0000
  231      VS3      4   VIR        VS3     87      0.0000      0.0000

Then if I want to set up a virtual site between the COG of 3 atoms do I
do it in the following way

[virtual_sitesn]
;site COG of three hydrogens at window
;site  i     j    k    func
229    7    40   58    1
230   10    25   55    1
231   28    37   52    1


Cheers

Gavin



Gavin Melaugh wrote:
> 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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>>
>>     
>
>