From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Fri Jun 12 2020 - 13:41:22 CDT
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--0000000000001b3aca05a7e76d2e--
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