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 - 13:42:29 CDT

Thank you so much for your explanation.
Jiali

On Fri, Jun 12, 2020 at 14:41 Josh Vermaas <joshua.vermaas_at_gmail.com> wrote:

> Exactly. Wrapping needs to be turned off. forceNoPBC just changes how
> colvars calculates distances internally. But since NAMD passes coordinates
> that are already wrapped, colvars will calculate a distance you didn't
> intend.
>
> -Josh
>
> On Fri, Jun 12, 2020 at 12:10 PM Jiali Wang <jwang204_at_binghamton.edu>
> wrote:
>
>> 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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