Re: Umbrella sampling colvars DistanceZ deviates a lot

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Sep 13 2016 - 11:23:56 CDT

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
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*"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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