Re: Re: colvar atom syntax

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Jun 16 2010 - 11:42:09 CDT

Mike:

Just a small addition to Giacomo's explanation. The "half-harmonic"
boundary potential is the following:

V(x) = 0.5 * k * (x - upperWall)^2 if x > upperWall
V(x) = 0 otherwise

and the default value of upperWall is upperBoundary.

Jerome

On 16 June 2010 18:20, Giacomo Fiorin <giacomo.fiorin_at_temple.edu> wrote:
> Hi Michael, upperBoundary is chosen by you.  There is no way to tell which
> is the highest possible RMSD value without knowing the system.  You chose 2
> Å for a specific reason (i.e. to keep the protein close to the ref
> structure), but in general it can be much higher.
>
> Anyway, the force will kick in only after RMSD goes above 2 Å: no matter how
> strong the force constant, you will always have some RMSD values a little
> over 2 Å.  There is no way to enforce it as a hard limit without using
> infinitely large forces (which is actually what would happen if the code
> were to automatically enforce the hard boundary).  However, you can control
> the tolerance by lowering or increasing upperWallConstant.
>
> Also, although you can set upperBoundary wherever you want, its more
> appropriate usage is as you suggested in your mail, as the highest
> theoretically possible above which the RMSD really never goes.  Use
> lowerWall, instead, to put, a wall on a smaller RMSD value, and keep in mind
> that you'll always have to allow for some tolerance.
>
> 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 Wed, Jun 16, 2010 at 11:24 AM, Michael Zimmermann <michaelz_at_iastate.edu>
> wrote:
>>
>> 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
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:03 CST