Re: Metadynamics problems

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri May 14 2021 - 10:43:08 CDT

Hello Alex, if the instability is sporadic you can safely restart and
continue running.

The instability, however, could be due to the relatively high rate at which
you add the Gaussian bias, 1 kcal/mol per 1000 steps. Not knowing the
specifics of the system, it would help you to figure out what are the
correlation times of the two dihedral angles from an equilibrium MD
trajectory, which you should already have. The variables may simply not
take up a bias that fast.

Lastly, you're using NAMD 2.12, which is more than 4 years old. While it's
true that the error is raised from a large force coming from Colvars, later
versions like 2.14 may handle it better, or at least clarify more clearly
the precise step where things go wrong. For Colvars specifically, there
are a few advantages for using metadynamics specifically:
https://urldefense.com/v3/__https://colvars.github.io/namd-2.14/colvars-refman-namd/colvars-refman-namd.html*sec:colvars_config_changes__;Iw!!DZ3fjg!tbDVuM83HD_04RzozxgF91FqHs3CWPrENr5oSpILZHhggFg8uG7aB3Ef24YVnREuRA$

Giacomo

On Fri, May 14, 2021 at 5:50 AM Alessandro Ruda <alessandro.ruda_at_su.se>
wrote:

> Dear *NAMD comunity*,
>
>
> I am running metadynamics on a set of two dihedral angles. I've tried
> default metadynamics and well tempered. For both of them after a few
> hours the run stops with errors like the following:
>
>
> *namd2:207125 terminated with signal 11 at PC=fc9213 SP=7ffe44263fa0.
> Backtrace:*
>
> */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]*
>
> */software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN12PmeRealSpace12fill_chargesEPPfS1_RiS2_PcS3_P11PmeParticle+0x2d43)[0xfc9213]*
>
> and the log file states:
>
> *mpprun info: Job terminated with error*
>
> Normal molecular dynamics works well so it must be related to
> metadynamics. This is the colvar file that i used:
>
> --------------------------------------------------------------------------------------------------------------------------------------
>
> *colvarsTrajAppend off*
>
> *colvar {*
> * name Psi*
> * width 2.5*
> * dihedral {*
> * group1 {*
> * atomnumbers { 32 }*
> * }*
> * group2 {*
> * atomnumbers { 22 }*
> * }*
> * group3 {*
> * atomnumbers { 20 }*
> * }*
> * group4 {*
> * atomnumbers { 21 }*
> * }*
> * }*
> * lowerBoundary -180*
> * upperBoundary 180*
>
> *}*
>
> *colvar {*
> * name Phi*
> * width 2.5*
> * dihedral {*
> * group1 {*
> * atomnumbers { 33 }*
> * }*
> * group2 {*
> * atomnumbers { 32 }*
> * }*
> * group3 {*
> * atomnumbers { 22 }*
> * }*
> * group4 {*
> * atomnumbers { 20 }*
> * }*
> * }*
> * lowerBoundary -180*
> * upperBoundary 180*
> *}*
>
> *metadynamics {*
> *wellTempered on*
> *biasTemperature 1490*
> *name metaPhiPsi*
> *colvars Phi Psi*
> *hillWeight 0.01*
> *hillwidth 1.0*
> *saveFreeEnergyFile no*
> *dumpFreeEnergyFile yes #When useGrids and this option are on, the PMF is
> written every colvarsRestartFrequency steps to the file outputName.pmf*
> *writeHillsTrajectory on*
> *newHillFrequency 100 *
>
> ---------------------------------------------------------------------------------------------------------------------------------------
>
> I have tried with different hillWeight values and the problem stays.
> Can I do something or should I restart from the last step and continue
> running and, in doing so,
> how can I keep the old colvars data so that I restart from the last points
> collected?
>
> Thank you in advance,
>
> All the best,
> Alex
>
>
>

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