Re: Re: colvar atom syntax

From: Michael Zimmermann (michaelz_at_iastate.edu)
Date: Wed Jun 16 2010 - 10:24:50 CDT

It looks like dos2unix fixed that initial error.

I've never had carriage control interfere with namd, so thanks for the
pointer.

It is still not clear to me how "upperBoundary" and "upperWallConstant" are
interpreted in a colvar that calculates RMSD. Is the upperBoundary the
greatest allowable RMSD? If so, how will it accomplish such a bound? Will
it increase the spring stiffness sufficient to not allow further RMSD
changes? Is the upperWallConstant then the greatest allowable spring
constant?

The user's guide gives more general descriptions:
*lowerWallConstant < (colvar) Lower wall force constant (kcal/mol) >
Description: If lowerWall or lowerBoundary is defined, provides the force
constant. The
energy unit of the constant is kcal/mol, while the spatial unit is that of
the colvar.
*upperWallConstant < (colvar) Upper wall force constant (kcal/mol) >
Description: Similar to lowerWallConstant.

Thanks again.

Mike Z

On Wed, Jun 16, 2010 at 7:24 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:

> Hi Mike,
>
> I cannot reproduce this error, something in the file seems to confuse
> the parser. If the file has been edited under windows at any point,
> you could try treating it with dos2unix.
>
> Another point, though: the last two keywords, "upperBoundary" and
> "upperWallConstant" are colvar-related, not colvar-component-related,
> so they should be outside the rmsd block (but still within the colvar
> block).
>
> Jerome
>
> On 15 June 2010 22:59, Michael Zimmermann <michaelz_at_iastate.edu> wrote:
> > 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
> >
>

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

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