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

From: Jiali Wang (jwang204_at_binghamton.edu)
Date: Thu Jun 11 2020 - 11:49:54 CDT

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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