From: Suranga Edirisinghe (nerangedi_at_gmail.com)
Date: Tue Aug 28 2012 - 13:45:03 CDT
Hi
I would let namd to use default parameters as mush as possible to start
with. Then slowly make changes as system runs smoothly.
Thanks
Suranga
On Tue, Aug 28, 2012 at 9:01 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Tue, Aug 28, 2012 at 3:07 PM, Mariana Graterol
> <marianagraterol_at_gmail.com> wrote:
> > Hello and thanks to all,
> >
> > After NPT run I can't restart the calculation, cause the "size cell" is
> too
> > big now. I know that in a molecular dynamics with pressure and
> temperature
> > controls, volume is not constant... but, my initial cell was 120 x 120 x
> 120
> > Angs., and then it increases until 1100 x1100 x 1100!
>
> which means that something went horribly wrong.
>
> you may want to run with fixed volume for a bit
> before you enable npt. also, you may need to
> run a minimization to reduce the potential energy.
>
> please check out the namd tutorials and their discussion
> of what kind of protocol to follow to set up a periodic
> system and why. this must not be followed blindly,
> but with adaptations for your specific system.
>
> axel.
>
>
> >
> > The structure file looks like the cubic box is losted, that is, all water
> > molecules are scattered around the protein a very large distance.
> > I have wrap all on, and langevin pressure control in my configuration
> file;
> > starting with a minimized structure and previously heated slowly until
> 300
> > K.
> >
> > Is it really my cell size? Why the "box" image is lost? Is it something
> > about coordinates or a mistake in setting npt conditions?
> >
> > Thank you for any comment that help me...
> >
> > ******
> > # Input files
> > coordinates C:\\Users\\pc\\Documents\\test.pdb
> > structure C:\\Users\\pc\\Documents\\test.psf
> > parameters parm.prm
> > paraTypeCharmm on
> >
> > # Output files
> > binaryoutput yes
> > outputname C:\\Users\\pc\\Documents\\test
> > restartfreq 1000
> > restartsave yes
> > binaryrestart yes
> > DCDfile C:\\Users\\pc\\Documents\\test.dcd
> > DCDfreq 1000
> > DCDUnitCell no
> > outputEnergies 1000
> > mergeCrossterms yes
> > outputMomenta 0
> > outputPressure 0
> > outputTiming 10000
> >
> > # Timestep parameters
> > numsteps 200000
> > timestep 1.000000
> > firsttimestep 0
> > stepspercycle 20
> >
> > # Simulation space partitioning
> > cutoff 12.000000
> > switching on
> > switchdist 8.000000
> > limitdist 0.000000
> > pairlistdist 14.000000
> > splitPatch hydrogen
> > hgroupCutoff 2.500000
> > margin 0.000000
> > pairlistMinProcs 1
> > pairlistsPerCycle 2
> > outputPairlists 0
> > pairlistShrink 0.010000
> > pairlistGrow 0.010000
> > pairlistTrigger 0.300000
> >
> > # Basic dynamics
> > exclude scaled1-4
> > temperature 300.000000
> > COMmotion no
> > zeroMomentum no
> > dielectric 1.000000
> > nonbondedScaling 1.000000
> > 1-4scaling 1.000000
> > vdwGeometricSigma no
> > seed 12345
> > rigidBonds none
> >
> > # PME parameters
> > PME on
> > PMETolerance 1.000000e-06
> > PMEInterpOrder 4
> > PMEGridSpacing 1.000000
> > PMEGridSizeX 120
> > PMEGridSizeY 150
> > PMEGridSizeZ 144
> > FFTWEstimate no
> > FFTWUseWisdom yes
> >
> > # Full direct parameters
> > FullDirect no
> >
> > # Multiple timestep parameters
> > fullElectFrequency 4
> > MTSAlgorithm impulse
> > longSplitting c1
> >
> > # Harmonic constraints
> > constraints on
> > consexp 2
> > conskcol B
> > constraintScaling 1.000000
> > conskfile C:\\Users\\pc\\Documents\\test.pdb
> > consref C:\\Users\\pc\\Documents\\test.pdb
> >
> > # Periodic boundary conditions
> > cellBasisVector1 117.002419 0.000000 0.000000
> > cellBasisVector2 0.000000 145.766808 0.000000
> > cellBasisVector3 0.000000 0.000000 143.076828
> > cellOrigin -0.000001 -0.000001 0.0000006
> > XSTfreq 1000
> > wrapWater off
> > wrapAll on
> > wrapNearest off
> >
> > # Langevin dynamics
> > langevin on
> > langevinTemp 300.000000
> > langevinHydrogen off
> > langevinDamping 5.000000
> >
> > # Interactive molecular dynamics
> > IMDon on
> > IMDport 3000
> > IMDfreq 20
> > IMDwait off
> > IMDignore off
> >
> > # Constant Pressure Control
> >
> > useGroupPressure no
> > useFlexibleCell no
> > useConstantArea no
> > langevinPiston on
> > langevinPistonTarget 1.01325
> > langevinPistonPeriod 100
> > langevinPistonDecay 50
> > langevinPistonTemp 300
> >
> >
> >
> > --
> > * mari *
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
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