Re: Re: MD run terminated with singnal 11

From: Alessandro Ruda (alessandro.ruda_at_su.se)
Date: Fri Oct 15 2021 - 08:56:04 CDT

Hi Josh,

yes, I checked them and they are ok, I just removed the entire path for the sake of clarity when I posted the question!

Thank you!

/alex

________________________________
From: Josh Vermaas <vermaasj_at_msu.edu>
Sent: 15 October 2021 15:30:05
To: namd-l_at_ks.uiuc.edu; Alessandro Ruda
Subject: Re: namd-l: Re: MD run terminated with singnal 11

Hi Alex,

Are you sure that you have the right structure, coordinates, bincoordinates, and binvelocities files? Those do not look sane to me.

-Josh

On 10/15/21 8:04 AM, Alessandro Ruda wrote:

It seems related to the PME parameters anyway. I tried to change parameters such as the size of the grid or the spacing from 0.5 to 1.5 but it didn't work as well.

Any hints on what could cause the instability?

All the best,

Alex

________________________________
From: Alessandro Ruda
Sent: 23 September 2021 15:46:31
To: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>
Subject: MD run terminated with singnal 11

Dear NAMD comunity,

I am running a simulation of a tetrasaccharide in salty water (0.2M NaCl - 50x50x50 wb) using Hydrogen Mass Repartition. I run a first minimization followed by heating and short equilibration (few us) but when I start the production it stops after few seconds with this error in slurm (i am running on a cluster).

  * namd2:37211 terminated with signal 11 at PC=fc9213 SP=7ffe9c9ee6a0. Backtrace:
  * namd2:37213 terminated with signal 11 at PC=fc9213 SP=7ffca5b2a120. Backtrace:
  * namd2:110002 terminated with signal 11 at PC=fc9213 SP=7ffe5edf3f20. Backtrace:
  * namd2:37217 terminated with signal 11 at PC=fc9213 SP=7ffe224b27a0. Backtrace:

..etc...etc....

  * 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]
  * /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]
  * /software/sse/manual/namd/2.12/i18/nsc1/namd2(_ZN10ComputePme6doWorkEv+0x1684)[0xb92d14]
  * /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(_ZN10ComputePme6doWorkEv+0x1684)[0xb92d14]

..etc...etc

please find attached file if needed.The log file simply states:

  * mpprun info: Job terminated with error

It happened to another simulation also with a very much similar tetrasaccharide and I managed to make it work by building the tetrasaccharide again, solvate it, minimize etc etc. It worked but I don't know why.
It didn't work for this one and every time I restart the simulation I get the same error.

This is the configuration file I am using:

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

structure /.pdf
coordinates /.pdb
bincoordinates /.coor
binvelocities /.vel

set temperature 300

firsttimestep 0

# Input
paraTypeCharmm on
parameters /Parameters/par_all36_carb.inp
parameters /Parameters/par_water_ions.inp
parameters /Parameters/par_all36_prot.inp
parameters /Parameters/par_all36m_prot.inp
parameters /Parameters/par_hbond.inp

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 16.0
margin 0

# Integrator Parameters
timestep 4.0 ;
rigidBonds all ;
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 20
pairlistsPerCycle 2
wrapWater on
wrapAll on

# Constant Temperature Control
langevin on ;
langevinDamping 1 ;
langevinTemp $temperature
langevinHydrogen off ;

# PME
PME yes
PMEGridSpacing 1.0

#manual grid definition
PMEGridSizeX 60
PMEGridSizeY 60
PMEGridSizeZ 60

# Constant Pressure Control (variable volume)
useGroupPressure yes ;
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 50.0
langevinPistonDecay 25.0
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 2500 ;# 2500steps = every 10ps
dcdfreq 2500 ;# = every 10ps
xstFreq 2500
outputEnergies 2500
outputtiming 2500
outputPressure 150
binaryoutput yes

extendedSystem /proj/carbohydratedynamics/users/x_aleru/LeA_LeX/Run_LeX4_HMR/3_equilibration/LeX4_heated.restart.xsc

run 125000000 ;# 500 ns
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

I really don't know what the problem is related to. Does anybody have some hints about it?

Thank you in advance,
Alessandro

--
Josh Vermaas
vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!ovA5jPIGK0ftfdPkI0iJDcW_ouWGbNnNoOhzWZAEwzMlu9jI6XCEvgP-0nJ0sERZpw$ 

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