From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Jun 12 2020 - 12:42:26 CDT
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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