From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Oct 30 2020 - 10:43:03 CDT
Ok, a couple thoughts here.
One, I hadn't noticed this before, but the nonbonded settings are a bit
daring. WIth 2 fs timesteps you're probably better off with short range
interactions every step, and full electrostatics every 2 or 3. This may be
causing the instability.
The seed should also be fixed as mentioned in my last email. If you just
delete the seed line NAMD will use a seed based on the current wallclock
time, which is appropriate and safe.
Also, why are you minimizing the system at each restart? This would not be
typical, and might be causing the crashes.
Best,
Peter
On Fri, Oct 30, 2020 at 11:09 AM Constantin Gunkel <alanka_at_hotmail.de>
wrote:
> @Peter Freddolino
>
> Thanks for the quick answer.
>
> Here is the first restart file. The rest look all the same, just
> importing the information of the last restart outputs and not the
> original one. I have also tried them without the extra new minimization
> steps below but nothing really works.
>
> Best,
>
> Constantin
>
> # input
> set input ../hoffnung/SI.restart
> coordinates ${input}.coor
> velocities ${input}.vel
> extendedSystem ${input}.xsc
> structure ../hoffnung/SI.psf
> parameters ../hoffnung/par_all36_prot.prm
> parameters ../hoffnung/par_all36_na.prm
> parameters ../hoffnung/par_all36_lipid.prm
> parameters ../hoffnung/par_all36_carb.prm
> parameters ../hoffnung/par_all36_cgenff.prm
> parameters ../hoffnung/toppar_water_ions_namd.str
> paratypecharmm on
>
> # output
> set output ../hoffnung/SI1
> outputname $output
> dcdfile ${output}.dcd
> xstFile ${output}.xst
> dcdfreq 10000
> xstFreq 10000
>
> binaryoutput no
> binaryrestart no
> outputEnergies 100
> restartfreq 1000
>
> fixedAtoms off
>
> # Basic dynamics
> exclude scaled1-4
> 1-4scaling 1
> COMmotion no
> dielectric 1.0
>
> # Simulation space partitioning
> switching on
> switchdist 9
> cutoff 10
> pairlistdist 12
>
> # Multiple timestepping
> firsttimestep 475000
> timestep 2
> rigidBonds all
> stepspercycle 20
> nonbondedFreq 2
> fullElectFrequency 4
>
> # Temperature control
>
> set temperature 325
>
> # Langevin Dynamics
> langevin on; # do langevin dynamics
> langevinDamping 1; # damping coefficient (gamma) of
> 1/ps
> langevinTemp $temperature; # bath temperature
> langevinHydrogen no; # don't couple langevin bath to
> hydrogens
> seed 12345
>
> # Pressure control
> langevinPiston on
> langevinPistonTarget 1.01325; # in bar -> 1.01325 bar = 1 atm
> langevinPistonPeriod 200
> langevinPistonDecay 100
> langevinPistonTemp $temperature
> useFlexibleCell no
> useGroupPressure yes
> fixedAtomsForces off
>
> # PBC
> wrapAll on
> wrapwater on
> dcdUnitCell yes
>
> PME yes
> PMEGridSizeX 120
> PMEGridSizeY 120
> PMEGridSizeZ 150
>
> # Extra Parameters
>
> margin 3
>
>
> # Scripting
> minimize 40000
>
> run 400000
>
>
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