Re: Metadynamics problems

From: Alessandro Ruda (alessandro.ruda_at_su.se)
Date: Mon May 17 2021 - 11:51:10 CDT

Thanks Giacomo for the prompt reply,

Restarting the run didn't really work since it stopped again after 20 minutes (after running for 11 h though). Doesn't look stable at all.

The correlation time for the torsions I am looking at is around 100 ps.

What value would you suggest to be the optimal one in such case?

All the best,

Alex

________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: 14 May 2021 17:43:08
To: NAMD list; Alessandro Ruda
Subject: Re: namd-l: Metadynamics problems

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!rjaeCr5aC3536OV2G4_FTzSKIEA6WZlT-zoXvc1VHCTUZDGKcghFS0LbSI8rSP1OpA$ <https://urldefense.com/v3/__https://colvars.github.io/namd-2.14/colvars-refman-namd/colvars-refman-namd.html*sec:colvars_config_changes__;Iw!!DZ3fjg!rjaeCr5aC3536OV2G4_FTzSKIEA6WZlT-zoXvc1VHCTUZDGKcghFS0LbSI8rSP1OpA$ >

Giacomo

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

o,
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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