Re: Re: colvar atom syntax

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Wed Jun 16 2010 - 11:20:33 CDT

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--00c09f93d92dc81bcc0489281b1d--

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