Re: Flat-bottom harmonic position restraints using colvars

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Feb 05 2020 - 12:51:05 CST

Hello Daipayan, those would work on the collective variables (i.e. one or a
few numbers for the entire system) as opposed to an entire set of Cartesian
coordinates. And in any case, it would be quite inefficient to run a
multitude of restraints via Colvars if they d don't need a collective
operation.

Check out the nightly build, because a similar feature for Cartesian
coordinates has just been added:
https://charm.cs.illinois.edu/gerrit/c/namd/+/5316

On Wed, Feb 5, 2020 at 1:29 PM Daipayan Sarkar <sdaipayan_at_gmail.com> wrote:

> Hello,
>
> My objective is to apply flat-bottom harmonic position restraints to the
> C-alpha (CA) atoms. To achieve this, I am using the colvars harmonicWalls.
> I have a question regarding setting the values of lower and upperWalls,
> with respect to the reference CA positions.
>
> Typically, a regular harmonic position restraint is applied, where a
> reference PDB is provided as an input to the parameter consref. My
> question, is can we pass a reference pdb to colvars and set the upper and
> lower bounds with respect to the selection?
>
> Following is my colvar definition. Any help is greatly appreciated.
>
> #########################
> colvars on
> colvarsTrajFrequency 100
>
> cv config "
> colvar {
> name calpha
> group1 {
> psfSegID AP1
> atomNameResidueRange CA 1-76
> }
> }
> "
>
> cv config "
> harmonicWalls {
> name fb_restraint
> colvars calpha
> lowerWalls * #add_lower_bound_from_ref_CA_position*
> upperWalls *#add_upper_bound_from_ref_CA_position*
> lowerWallConstant 10.0
> upperWallConstant 10.0
> }
> "
> #########################
>
>
> Thanks,
> Daipayan
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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