From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Wed Jun 10 2020 - 15:10:35 CDT
Giacomo or Jerome can correct me if I'm wrong, but I believe that your main
wrapping options the the larger NAMD configuration file may be overriding
the PBC behavior within the Colvars module, since colvars depends on NAMD
to pass along the coordinates. Usually there is a warning during NAMD
startup if this is the case, but alot of users gloss over this. Do you have
"wrapAll" turned on in your main NAMD configuration file?
-Josh
On Wed, Jun 10, 2020 at 11:57 AM Jiali Wang <jwang204_at_binghamton.edu> wrote:
> Dear NAMD users,
> Good afternoon, I am using harmonic force to push two atom together, with
> set a colvars to tracking the distance from around 50A to 0A. However, even
> I set "forceNoPBC on", but the moving atom still jump from center
> simulation box to other periodic environments, detail setting as following,
> is there something wrong in my file?
> I want to track the distance and save into frames to run the potential
> mean force calculations.
> best,
> Jiali
>
>
> colvarsTrajFrequency 500
> colvar {
> name length
> outputAppliedForce off
>
> distance {
> forceNoPBC on
> group1 {
> atomNumbers 18937
> }
> group2 {
> atomNumbers 91692
> }
> }
> }
> harmonic {
> name lenpot
> colvars length
> forceConstant 20 # in kcal/mol/A^2
> forceNoPBC yes
>
> centers 56 # go from 25 Angstrom RMSD...
> targetCenters 0 # ... to 1 Angstrom
> targetNumStages 20 # n-1 steps of calculation
> targetNumSteps 20000 #[expr total ${numsteps} / 10
> targetnumberstages]
> outputCenters on
>
>
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