Re: [External Email] Re: how to disable the periodic condition tracking two atom distance

From: Jiali Wang (jwang204_at_binghamton.edu)
Date: Fri Jun 12 2020 - 13:10:20 CDT

Dear Jerome,
Thank you for your reply. I am trying to push two atoms together from a 50A
to 3A distance. I finally found the atoms jump from different periodic
boxes, not only in the large range, but also happened when distance around
10A. I set "forceNoPBC on" and "wrap on". Do you mean I need to disable the
"wrap on" option?
best,
Jiali

On Fri, Jun 12, 2020 at 1:42 PM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Jiali,
>
> Why do you want to use forceNoPBC in the first place? Is the distance you
> want to measure larger than half the box size?
> If so, then you should enable forceNoPBC, but disable wrapping, especially
> if you run the simulation in several NAMD runs.
>
> Jerome
>
>
> ----- On 11 Juin 20, at 18:49, Jiali Wang jwang204_at_binghamton.edu wrote:
>
> > Dear Josh,
> > Thank you so much for your reply. WrapALL is on. I am not sure what
> > happened. but I found colvar tracking traj distance is not affected by
> > jumping to periodic boxes. So I supposed PMF will not affected by this.
> is
> > that correct?
> > best.
> > Jiali
> >
> > On Wed, Jun 10, 2020 at 4:10 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
> > wrote:
> >
> >> 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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