Re: Umbrella sampling colvars DistanceZ deviates a lot

From: Tabris Chun Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Tue Sep 13 2016 - 12:27:25 CDT

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 (mailto: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 (mailto: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 (tel:+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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