Re: change in box geometry for simulation of pure water

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Aug 27 2008 - 22:58:07 CDT

What, exactly, is the error you get when it crashes? If it's just a
"periodic dimensions have become too small for patch grid" error, you
can just restart and be fine. Depending on what kind of system you're
trying to model you might now want to bother with having useflexiblecell on.
Peter

maria goranovic wrote:
> Hello,
>
> I ran a simulation of a box of water with a standard config file using
> useconstantratio and useflexiblecell. However, the simulation box
> becomes thinner in one dimension, until the simulation crashes. Why
> does this happen?
>
> Thanks for the suggestions, config file below:
>
> !!!!!!!!!!!!!!!!!!!!!!!!!
> set MOL wat2
>
> set temp 310
>
> set xbox 39.97
> set ybox 39.94
> set zbox 39.94
>
> structure ${MOL}.psf
> coordinates ${MOL}.pdb
> temperature 0
> parameters par-combined.prm
> paraTypeCharmm on
>
> outputEnergies 5000
> outputTiming 5000
> xstFreq 5000
> dcdFreq 5000
> wrapAll on
> margin 5
>
> rigidbonds on
> timestep 2
> nonBondedFreq 1
> fullElectFrequency 1
> stepsPerCycle 20
>
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchDist 10
> cutoff 12
> pairlistdist 14
>
> cellBasisVector1 $xbox 00.00 00.00
> cellBasisVector2 00.00 $ybox 00.00
> cellBasisVector3 00.00 00.00 $zbox
>
> #########################################
> cellOrigin 0.05952 0.09806 -0.1598
>
> Pme on
> PmeGridsizeX 40
> PmeGridsizeY 40
> PmeGridsizeZ 40
>
> #########################################
> # PRESSURE AND TEMPERATURE CONTRON
> #########################################
>
> # temperature
> langevin on
> langevinDamping 5
> langevinTemp $temp
> langevinHydrogen no
>
> useflexiblecell yes
> useconstantratio yes
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 100
> langevinPistonDecay 50
> langevinPistonTemp $temp
>
> binaryoutput on
> outputname ${MOL}-equil
>
> # INITIAL ENERGY
> minimize 0
>
> minimize 5000
> output ${MOL}-min1
>
> #########################################
> # HEAT
> #########################################
>
> set tem 310
> langevinTemp $tem
>
> for {set p 1 } { $p < 11 } { incr p } {
> run 1000000
> output ${MOL}-$p
> }
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen

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