change in box geometry for simulation of pure water

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Wed Aug 27 2008 - 07:48:12 CDT

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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