Re: Re: colvar atom syntax

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Thu Jun 10 2010 - 17:20:18 CDT

Michael: again, which version of NAMD are you using? There isn't
unfortunately a wide set of examples currently available, but the NAMD 2.7b2
Users Guide contain exactly the example you're looking for, with two atomic
distances and an harmonic restraint applied to both. You just need to fill
in the atom numbers and the distance values that you want to restrain.

If you have too many interatomic distances to restrain, you may also try the
"rmsd" variable and apply a harmonic potential to it, with center on zero.

Giacomo

---- ----
 Dr. Giacomo Fiorin
 ICMS - Institute for Computational Molecular Science - Temple University
 1900 N 12 th Street, Philadelphia, PA 19122
 giacomo.fiorin_at_temple.edu
---- ----

On Thu, Jun 10, 2010 at 4:15 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
>

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