Re: Atom velocities too high.

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Sun Oct 19 2008 - 11:48:34 CDT

Hi Diego,

I'd be more tempted to blame only minimizing for 100 steps, or
shooting the system straight to 310 K, or using a 2.0 fs time step
without rigid bonds. You probably need to address all three of these
issues. You should be able to find solutions/discussions about all of
these on the list archive and in the various tutorials that are
available.

Good luck.

Josh

On Oct 19, 2008, at 7:59 AM, Diego Alejandro Vargas wrote:

> Hi everybody,
> I am running a minimization and equilibration simulation on fascin
> in a water box. The simulation begins to run, but stops after a
> while because atom velocities are above the allowed limit.
>
> I don't understand why this is the case. I am tempted to blame
> leaving bonds to hydrogen non-rigid and not applying Langevin
> dynamics to the hydrogens (ridigBonds none - langevinHydrogen off).
> Would applying Langevin dynamics to the hydrogen be better but more
> computationally expensive? Below is my configuration file, in case
> it may be of help.
>
> Thank you for your attention,
> Diego A. Vargas
>
> _______________________________________________________________
>
> structure ***
> coordinates ***
>
> set temperature 310
> set outputname ***
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
> temperature $temperature
>
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
> timestep 2.0
> rigidBonds none
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on
> langevinDamping 5
> langevinTemp $temperature
> langevinHydrogen off
>
>
> # Periodic Boundary
> cellBasisVector1 48. 0. 0.
> cellBasisVector2 0. 58. 0.
> cellBasisVector3 0. 0 46.
> cellOrigin 62. 89. 10.
>
> wrapAll on
>
>
> PME yes
> PMEGridSizeX 50
> PMEGridSizeY 50
> PMEGridSizeZ 50
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
>
>
> outputName $outputname
>
> restartfreq 500
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> minimize 100
> reinitvels $temperature
>
> run 250000 ;# 500ps
>
>

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
------------------------------------------------------------------------------------------------------

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