From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Oct 19 2021 - 19:32:22 CDT
Are you sure “/.pdf” is your psf file? There are multiple reasons, I’m 95%
sure that is not the correct file name.
Jeff
On Fri, Oct 15, 2021 at 08:58 Alessandro Ruda <alessandro.ruda_at_su.se> wrote:
> 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
> *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 $outputname
>
> restartfreq 2500 ;# 2500steps = every 10ps
> dcdfreq 2500 ;# = every 10ps
> xstFreq 2500
> outputEnergies 2500
> outputtiming 2500
> outputPressure 150
> binaryoutput yes
>
>
> extendedSystem
> /proj/carbohydratedynamics/users/x_aleru/LeA_LeX/Run_LeX4_HMR/3_equilibration/LeX4_heated.restart.xsc
>
> run 125000000 ;# 500 ns
> ----------------------------------------------
> ----------------------------------------------
> ----------------------------------------------
> ----------------------------------------------
> ----------------------------------------------
>
> I really don't know what the problem is related to. Does anybody have some
> hints about it?
>
> Thank you in advance,
> Alessandro
>
>
>
>
>
>
> --
> Josh Vermaas
> vermaasj_at_msu.edu
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
> Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-vermaas/ <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!ovA5jPIGK0ftfdPkI0iJDcW_ouWGbNnNoOhzWZAEwzMlu9jI6XCEvgP-0nJ0sERZpw$>
>
> --
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Associate Professor
Department of Anatomy and Physiology
Kansas State University
Office: 334 Coles Hall
Phone: 785-532-6311
Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!q2fiX8UD1ps11Uo5FeQxorcgPUXVFyXZhL6aMz0X3SBUBKS6eRnfQ0iuEBLaPazcbg$
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