From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Sep 13 2016 - 15:16:14 CDT
Hi Kevin, the wrapping is only done in the file, not in the memory during a
run. Thus, any wrapping issue would only arise when the restart file is
read by the next run.
On Tue, Sep 13, 2016 at 1:27 PM, Tabris Chun Chan <
cchan2242-c_at_my.cityu.edu.hk> wrote:
> Hi Fiorin, thank you for the hints. However, I am wondering if it is the
> case, shouldn't colvars meaure the value after NAMD unwrapping the restart
> coordinates? If it is really reading a wrapped value, what will happen when
> it couples a wrapped value to the window center during a unwrapped run?
> Hard to imagine.
>
> Many thanks!
>
> Regards,
> Kevin
>
>
> On 14 Sep 2016, 00:24 +0800, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>,
> wrote:
>
> Hello Kevin, try looking into possible PBC wrapping issues. Coordinates
> are internally unwrapped during a run, but get wrapped when an output file
> (such as a restart is written) and this will affect the next run.
>
>
>
> On Tue, Sep 13, 2016 at 12:19 PM, Kevin C Chan <
> cchan2242-c_at_my.cityu.edu.hk> wrote:
>
>> Dear Users,
>>
>> I am doing umbrella sampling in NAMD with the colvars function. I have
>> specify a colvars file like this:
>> colvarsTrajFrequency 20
>> colvarsRestartFrequency 1000
>>
>> colvar {
>> name ProjectionZ
>>
>> width 1.0
>>
>> distanceZ {
>> main {
>> atomsFile ../main.pdb
>> atomsCol B
>> atomsColValue 1.0
>> }
>> ref {
>> atomsFile ../ref.pdb
>> atomsCol B
>> atomsColValue 1.0
>> }
>> forceNoPBC yes
>> }
>> }
>>
>> harmonic {
>> colvars ProjectionZ
>> centers 59.5
>> forceConstant 4.0
>> }
>>
>> Pretty standard. The first three lines of colvars.traj reads:
>> 0 5.96855721722479e+01
>> 20 5.96916027979287e+01
>> 40 5.96942978400560e+01
>> Pretty close. The last three lines of colvars.traj reads:
>> 499940 5.91646234042935e+01
>> 499960 5.91735242021637e+01
>> 499980 5.91815463732824e+01
>> Also close. Good. However, strange things happen when I restart the
>> simulation over and over again from restart.coor, restart.vel and
>> restart.xsc files.
>> After a few times (~70) of restarts. While the last three lines of another
>> colvars.traj reads:
>> 606960 5.95480754008586e+01
>> 606980 5.95456901525873e+01
>> 607000 5.95617980942163e+01
>> The first three lines of the next colvars.traj reads:
>> 0 6.33546567861433e+01
>> 20 6.33540970478523e+01
>> 40 6.33519859940328e+01
>> which was pretty far away from what I want. Then I can see the colvars
>> shifting the value towards 5.95. Then for the next colvars.traj:
>> 0 4.86674663226018e+01
>> 20 4.86540561800189e+01
>> 40 4.86566065988872e+01
>>
>> There seems to have something wrong with restarting simulations with
>> colvars turned on. Anyone has experience on this?
>>
>> Thanks in advance.
>>
>> Regards,
>> Kevin
>> City University of Hong Kong
>> ukevi_at_gmx.hk
>>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
>
> Scholar: http://goo.gl/Q3TBQU
> Personal: http://giacomofiorin.github.io/
> Lab page: https://icms.cst.temple.edu/members.html
>
> *"As computer programmers we have a responsibility to make sure that we
> run the computers instead of the computers running us."* - Steve Oualline
>
>
>
-- Giacomo Fiorin Associate Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."* - Steve Oualline
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