[gmx-users] virtual sites set up for topology file
Gavin Melaugh
gmelaugh01 at qub.ac.uk
Fri May 6 13:27:08 CEST 2011
Hi Justin
Thanks for the reply. To create a virtual site at the centre of geometry
of 3 atoms, according to the manual, do you not say: [virtual_sitesn],
the index of the site, the index of the three atoms and then the
function type 1 which determines that it is COG.
Or as I now realise. State [virtual_site3], site index atom indices, and
function 1. The fact that there are no parameters then by default must
mean it is COG. Is this correct?
Gavin
Justin A. Lemkul wrote:
>
>
> 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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>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
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