[gmx-users] virtual sites set up for topology file
Gavin Melaugh
gmelaugh01 at qub.ac.uk
Fri May 6 12:36:28 CEST 2011
Hi
Having tried to run grompp using the data below I keep getting the
following error
Fatal error:
Unknown vsiten type 7
Does anyone know why this might be?
Gavin
Gavin Melaugh wrote:
> 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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>>>
>>>
>>
>>
>
>
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