Re: colvar atom syntax

From: Michael Zimmermann (michaelz_at_iastate.edu)
Date: Thu Jun 10 2010 - 15:40:53 CDT

Dear NAMD users,

My apologies, the simulation does fail immediately when the colvar
configuration file is not set. So, again, if there is some more through
documentation on the colvar config file I would appreciate being pointed to
it.

On Thu, Jun 10, 2010 at 3:15 PM, Michael Zimmermann <michaelz_at_iastate.edu>wrote:

> I am having trouble finding an example colvarsConfig file. NAMD Some of
> the Colvar documentation says that the format is similar to a regular NAMD
> configuration file, but what parameters need to be set in it?
>
> All I want is to restrict the internal motion of a subset of atoms in my
> simulation. I do not want them fixed in space, but I want their relative
> positions to remain roughly unchanged.
>
> I do not have the colvarsConfig parameter set (no calvar config file) and
> the simulation has not thrown any errors.
>
> Mike
>
>
> On Tue, Jun 8, 2010 at 1:11 PM, Michael Zimmermann <michaelz_at_iastate.edu>wrote:
>
>> Dear NAMD users,
>>
>> I am having trouble finding the proper syntax for atom assignments within
>> colvars. I want to keep a group of atoms that are in different segments
>> constrained by RMSD to a reference position. This is what I have in my
>> config file so far, but there seems to be something wrong...
>>
>> ================================
>> colvars on
>> colvar {
>> rmsd {
>> atoms {
>> psfSegID P6
>> atomNameResidueRange 231-235
>> psfSegID P16
>> atomNameResidueRange 232-235
>> psfSegID P29
>> atomNameResidueRange 232-235
>> psfSegID P33
>> atomNameResidueRange 25-28
>> psfSegID P33
>> }
>> refPositionsFile markedProt.colvar.pdb
>> refPositionsCol B
>> }
>> }
>> ================================
>>
>> --
>> Michael Zimmermann
>> Ph.D. student in Bioinformatics and Computational Biology
>> Department of Biochemistry, Biophysics and Molecular Biology
>> Iowa State University
>>
>
>
>
> --
> Michael Zimmermann
> Ph.D. student in Bioinformatics and Computational Biology
> Department of Biochemistry, Biophysics and Molecular Biology
> Iowa State University
>

-- 
Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University

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