Re: Re: colvar atom syntax

From: Michael Zimmermann (michaelz_at_iastate.edu)
Date: Tue Jun 15 2010 - 15:59:09 CDT

Thank you all for your replies thus far. I am making progress, but still
running into problems with the RMSD colvar.

I am running NAMD version 2.7b2 Linux-x86_64.

------------------------------------------------------------
---> The contents of my colvar.conf file is:
------------------------------------------------------------
colvar {
    name RMSDColvar1
    rmsd {
        atoms {
            # this file has occupancy marked as 2 for the atoms
            # we want restrained by RMSD
            atomsFile prot.colvar.mark.pdb
            atomsCol O
            atomsColValue 2.0
        }
        refPositionsFile prot.colvar.mark.pdb
        refPositionsCol O
        refPositionsColValue 2.0
        upperBoundary 2 # does this mean the RMSD won't go above 2A?
        upperWallConstant 10 # is this the force constant used on springs to
restrain the atom group?
    }
}

------------------------------------------------------------
---> I don't know what the error I receive means. All my parameters have a
value as far as I can tell
------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "colvar1" [default]
colvars: Initializing a new "RMSD" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: Initializing atom group "atoms".
colvars: Error: keyword "" is not supported, or not recognized in this
context.
colvars: If this error message is unclear, try recompile with
-DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
------------------------------------------------------------

Any advice on how to continue would be appreciated.

Mike Z

On Thu, Jun 10, 2010 at 5:20 PM, Giacomo Fiorin
<giacomo.fiorin_at_temple.edu>wrote:

> 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
>>
>
>

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

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