From: Alessandro Ruda (alessandro.ruda_at_su.se)
Date: Fri May 14 2021 - 04:48:18 CDT
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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