Re: Distance restraints

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Oct 04 2019 - 07:01:46 CDT

Hello Paula, extraBonds is the way to go for fixed distance restraints
on *individual
atoms*
http://www.ks.uiuc.edu/Research/namd/2.13/ug/node27.html#SECTION00086400000000000000

If you want to apply restraints to *groups of atoms*, then you'll need
Colvars, using a distance variable and a harmonic restraint:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvar
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_distance
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_harmonic

Giacomo

On Fri, Oct 4, 2019 at 3:23 AM Paula Mihaljevic-Juric <
paula.mihaljevic-juric_at_polytechnique.edu> wrote:

> Hi
>
> Can I apply distance restraints in a same way secondary structure
> restraints are applied in MDFF or do I have to use colvars variables to
> apply them?
>
> I wanted to define in a separate files with fc and reference distance for
> each atom and use sth like
>
> if {$EXTRAB != 0} {
> extraBonds yes
> foreach fil $EXTRAB {
> extraBondsFile $fil
> }
> }
>
> To read them. Would this be sufficient?
>
> If I am not able to use this, how can I define distance restraints using
> colvars, I would appreciate some explaining me the procedure including what
> am I supposed to put in the pdf file.
>
> Thank you
> Paula
>
>

-- 
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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