Re: well-tempered metadynamics deforms the water box and the system becomes unstable..

From: zeynab hosseini (
Date: Wed Oct 21 2020 - 13:03:28 CDT

Hi Giacomo,

Thank you so much for your guidance.

On Wed, Oct 21, 2020 at 11:26 AM Giacomo Fiorin <>

> Hi Zeynab, the bias isn't correctly restarted because there is no command
> in there to load the state file.
> Quite simply, that tutorial shows how to do a quick metadynamics run for
> demonstration purposes, so it did not provide you with instructions on how
> to restart it. You can find these here:
> and pretty much it boils down to using either "colvarsInput" or "cv load
> ...." in the NAMD script to give restart information to Colvars.

I did as you said; including the "colvarsInput" command in the namd .conf
file to load the state file from previous simulation:

colvars on
colvarsInput cnt-ser_meta_29.colvars.state

I checked for the .hills.traj outputs of two dependent jobs. Here is the
result where I compared the last line of the .hill.traj file for the 29ns
and the first line of the same for the 30ns:

-tail cnt-ser_meta_*29*.colvars.meta-distance.hills.traj
      499000 2.31048448549163e+01 4.00000000000000e-03
      499250 2.35892630640388e+01 4.00000000000000e-03
      499500 2.26889661523101e+01 4.00000000000000e-03
      499750 2.31630224461575e+01 4.00000000000000e-03
      500000 2.30916666324611e+01 4.00000000000000e-03
 -head cnt-ser_meta_*30*.colvars.meta-distance.hills.traj
      500000 2.30916666324611e+01 4.00000000000000e-03
      500250 2.30432359543864e+01 4.00000000000000e-03
      500500 2.30443231967936e+01 4.00000000000000e-03
      500750 2.34415977600652e+01 4.00000000000000e-03

As it is seen, the hill weight on the 500000th time step (30ns) is not
started from the first step hill weight (0.1 kcal/mol) but it changed a
little from 29ns to 30ns. For 29ns, it is 4.50554516054642e-02, and for the
30ns, it is 4.27859620060334e-02. I wonder why they aren't exactly the same
and if this affects the convergence.

> This information is a bit harder to find in the NAMD manual, because the
> entire Colvars doc is crammed into one section of the NAMD manual. Also,
> in the NAMD website the links to the same sections are not consistent
> between NAMD versions, which throws off the search engines when searching
> the mailing list archives. For this reason, using the Colvars doc page
> linked above or the PDF version
> <> would be more
> appropriate.

Thank you.

All the best,

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