Re: colvar restraint simulation

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Feb 25 2019 - 11:40:17 CST

Hi Prabir, the documentation is here:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_harmonic

The restraints that you define will only be applied to the selected
variables, i.e. 5 and 1 respectively. Check, however, for typos, because
you have a couple.

Giacomo

On Mon, Feb 25, 2019 at 12:08 PM Prabir Khatua <prabir07chem_at_gmail.com>
wrote:

> Hi NAMD users,
>
> I want to do a distance restraint simulation where I need to use different
> force constants
> for different distance variables. I am using the following configuration
> file
>
> colvar {
> name d1
> distance {
> group1 { atomNumbers 3608} # A6 I31:O
> group2 { atomNumbers 566} # A1 V39:N
>
> }
> }
>
> colvar {
> name d2
> distance {
> group1 { atomNumbers 2462}
> group2 { atomNumbers 2963}
>
> }
> }
>
> colvar {
> name d3
> distance {
> group1 { atomNumbers 2439}
> group2 { atomNumbers 3106}
>
> }
> }
>
> harmonic {
> colvars d1 d2
> centers 3.5 3.5
> force constant 5.0
> }
>
> harmonic{
> colvars d3
> centers 4.0
> force constant 1.0
> }
>
> I am wondering whether simulation will apply a force constant of 5.0 on d1
> and d2, while
> 1.0 on d3. Please let me know if I am doing wrong and suggest me how to do
> it.
> Any suggestion would be appreciated.
>
> Thanks,
>
> Prabir
>
> *Prabir Khatua*
> *Postdoctoral Research Associate*
> *Department of Chemistry & Biochemistry*
> *University of Oklahoma*
> *Norman, Oklahoma 73019*
> *U. S. A.*
>
>
>
>
>
>
>
>
>
>

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

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