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
<symasha...@gmail.com <mailto:symasha...@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
<gmelaug...@qub.ac.uk <mailto:gmelaug...@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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