Re: Problem

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Oct 29 2020 - 06:57:17 CDT

Dear Constantin,
Just to make sure we can tell what is going on, can you please also post
the config file for one of your restarts?
Also, please note that a fixed seed should not be used in your restarts -
see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632580/
Best,
Peter

On Wed, Oct 28, 2020 at 10:14 PM Constantin Gunkel <alanka_at_hotmail.de>
wrote:

> Hello everyone.
>
> I have created a membrane System of 140 x 140 lipids with 4 Melittin
> Peptides above. The system is solvated and neutralized. The plan was to
> let it run for at least 60 ns meaning 2fs per timestep so all in all
> 30000000 steps with a minimization of 30000 (all NPT). I increased the
> temperature slowly every 3000 steps starting at 60 K to 325 K.
>
> I have 2 main problems. Every now and then I get the error:
>
> fatal error: periodic cell has become too small for original patch grid!
>
> The error became less frequent after i used the "margin 3" command in
> the config file.
>
> Also i used the restart files to continue which helped yet the error
> still happens sometimes and its still annoying. However my biggest
> problem is this:
> ERROR: Constraint failure in RATTLE algorithm for atom XXXX!
>
> I used the same method as above. Restarting at the last checkpoint. I
> can do about 200000-300000 steps before it crashes. However I am at
> 1756000 and the restart does absolutely nothing. I immediately get the
> second error. If one of you could help me or maybe has a similar problem
> I really would appreciate the advise. It is very import for me to get
> this simulation run.
>
> Constantin Gunkel
>
> original config file:
>
> # input
> coordinates ../hoffnung/SI.pdb
> 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/SI
> outputname $output
> dcdfile ${output}.dcd
> xstFile ${output}.xst
> dcdfreq 10000
> xstFreq 10000
>
> binaryoutput no
> binaryrestart no
> outputEnergies 1000
> 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 0
> timestep 2
> rigidBonds all
> stepspercycle 20
> nonbondedFreq 2
> fullElectFrequency 4
>
> # Temperature control
>
> set temperature 325
> temperature $temperature; # initial temperature
>
> # 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 $temperature
> useFlexibleCell no
> useGroupPressure yes
> fixedAtomsForces off
>
> # PBC
> cellBasisVector1 140 0.0 0.0
> cellBasisVector2 0.0 140 0.0
> cellBasisVector3 0.0 0.0 180
> cellOrigin 0.6 3.46 -40
> wrapAll on
> dcdUnitCell yes
>
> PME yes
> PMEGridSizeX 125
> PMEGridSizeY 120
> PMEGridSizeZ 160
>
> # Extra Parameters
> margin 3
>
> # Scripting
>
> minimize 50000
> reinitvels 60
> for {set t 60 } {$t <= $temperature} {incr t} {
> run 3000
> langevintemp $t
> }
> run 3000000
>
>
>

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