Umbrella sampling colvars DistanceZ deviates a lot

From: Kevin C Chan (
Date: Tue Sep 13 2016 - 11:19:08 CDT

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
      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.

City University of Hong Kong

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