Re: Applying a positional restraint with colvars module

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Mon Aug 16 2010 - 16:26:23 CDT

Dear Brigitte, I believe the script you want to use will do exactly what you
want. If the molecule is within the -5:5 interval from the beginning of the
simulation, you should have no problems whatsoever.

One suggestion: colvarsRestartFrequency can be higher, you don't need to
save at the same frequency of the trajectory (colvarsTrajFrequency). Think
of that as the same difference between the NAMD restart frequency and DCD
frequency: the former should be much higher (in number of steps) than the
latter, to minimize disk I/O.

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 Mon, Aug 16, 2010 at 1:06 PM, <bkziervogel_at_uchicago.edu> wrote:

> Hi,
>
> I have a question regarding the colvars function of NAMD.
>
> I am trying to run a simulation of a small molecule in a
> membrane channel. I would like to enforce a positional
> restraint on the small molecule to constrain it at a certain
> position along the channel axis (z-axis) for initial
> equilibration. I found a NAMD tutorial that did a similar
> thing by confining an ion within a sphere of a given radius
> (In Silico alchemy: A tutorial for alchemical free-energy
> perturbation calculations with NAMD) using the colvars module.
> I therefore tried to follow a similar protocol, but I wanted
> to be sure that I’m thinking about this and setting up my
> ColvarsConfig in the right way.
>
> Here is my ColvarsConfig…
>
> colvarsTrajFrequency 100
> colvarsRestartFrequency 100
>
> colvar {
> name colvar1
>
> width 0.1
>
> lowerboundary -15.0
> upperboundary 15.0
>
> lowerWall -5.0
> upperWall 5.0
>
> lowerWallConstant 100.0
> upperWallConstant 100.0
>
> distanceZ {
> main {
> atomsFile amp_main.ref
> atomsCol B
> atomsColValue 1.0
> }
> ref {
> atomsFile ref.ref
> atomsCol B
> atomsColValue 1.0
> }
> axis (0.0, 0.0, 1.0)
> }
> }
>
>
> Here, my “main” atomsfile includes all the atoms of my small
> molecule and my “ref” atomsfile contains atoms of 6 protein
> residues of the membrane channel. What I am hoping that this
> script does is to apply a harmonic potential on the COM of the
> small molecule using a force constant of 100 kcal/mol to
> restrain it within 10 angstroms (5 angstroms above and 5
> angstroms below) of the COM of the 6 protein residues along
> the z-axis.
>
> Could you please let me know if I am on the right track and
> applying this script in the right way?
>
> Thank you!!
>
> Brigitte
>
>

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