From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Jul 24 2013 - 15:25:06 CDT
What have you attempted in terms of troubleshooting beyond just changing
the number of steps? For instance, if I were in your position, since
nobody else seems to have this problem, and the previous responses
suggested this seems extremely odd, I would attempt to diagnose if this was
because of my molecular system or my computer system.
So:
1) can you do minimization normally to any arbitrary number of steps with a
different system such as one from the tutorials, but using all the same
input parameters you have here (i.e. just a different psf)?
2) what happens if you move your directory over to another computer, and
use the precompiled binaries there? Does it still stall out? You can even
just test it on a friend's laptop or something, since the binaries are
pretty small and your inputs here should also be.
~Aron
On Wed, Jul 24, 2013 at 4:12 PM, venkata agasthya <kvagasthya_at_gmail.com>wrote:
> Hello everyone,
>
> I have mailed in this group before about my problem with minimizing the
> energy of a protein/water system. I have tried running the minimization
> script using 500, 1000 and 10000 steps but the run gets stuck at a
> particular step and doesn't continue. It reaches a certain step and get's
> stuck. do anyone know why this happens.
>
> This is my minimization config file
>
> ###################################################
> # ESTROGEN RECEPTOR:
> ###################################################
>
>
> # MD SETUP
>
> timestep 2.0
> numsteps 1000
>
>
> # FLEXIBLE CELL
>
> useflexiblecell no
>
>
> # PSF
>
> structure protein.psf
>
>
> # FORCE FIELD
>
> parameters /work/agasthya/testing/par_all27_prot_lipid.prm
> paraTypeCharmm on
>
>
> # INPUT
>
> coordinates protein.pdb
>
>
> # PBC
>
> CellBasisVector1 50 0 0
> CellBasisVector2 0 50 0
> CellBasisVector3 0 0 50
> CellOrigin 0 0 0
>
>
> # OUTPUT
>
> outputenergies 100
> outputtiming 100
> outputpressure 100
> restartfreq 100
> XSTFreq 100
>
> outputname minimization_0
> restartname minimization
> binaryrestart yes
> binaryoutput no
>
>
> # PME
>
> PME yes
> PMETolerance 10e-6
> PMEInterpOrder 4
>
> PMEGridSpacing 1
>
>
> # WRAP
>
> wrapAll on
>
>
> # CONSTANT-T
>
> temperature 300.0
>
> langevin on
> langevinTemp 300.0
> langevinDamping 1.0
>
>
> # CONSTANT-P
>
> LangevinPiston on
> LangevinPistonTarget 1
> LangevinPistonPeriod 75
> LangevinPistonDecay 25
> LangevinPistonTemp 300
> StrainRate 0.0 0.0 0.0
> useGroupPressure yes
>
>
> # SPACE PARTITIONING
>
> splitpatch hydrogen
> hgroupcutoff 2.8
> stepspercycle 20
> margin 1.0
>
>
> # CUT-OFFS
>
> switching on
> switchdist 8.0
> cutoff 9.0
> pairlistdist 10.0
>
>
> # RESPA
>
> #fullElectFrequency 2
> #nonbondedFreq 1
>
>
> # 1-4 NON-BONDED
>
> exclude scaled1-4
> 1-4scaling 1.0
>
>
> # COM
>
> commotion no
>
>
> # SHAKE
>
> rigidbonds all
> rigidtolerance 0.000001
> rigiditerations 400
>
>
> # MINIMIZATION
>
> minimize 1000
>
> Thanks,
> Agasthya.
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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