[gmx-users] virtual sites set up for topology file
Justin A. Lemkul
jalemkul at vt.edu
Fri May 6 13:11:29 CEST 2011
Gavin Melaugh wrote:
> 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?
>
Your [virtual_sites] directive is not correct, either in its name (no such thing
as "virtual_sitesn" - the "n" should be replaced by a digit indicating the type)
or in the contents. See manual section 5.2.2.
-Justin
> 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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>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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