Re: Namd list: "Size cell" for restart

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 28 2012 - 11:01:51 CDT

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.

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:58 CST