water box getting deformed

From: sunita gupta (sunita.bio_at_gmail.com)
Date: Thu Dec 11 2008 - 07:06:30 CST

I am simulating a protein around 350 residues. The minimization and heating
went fine, but after equilibrating the system for 200 ps, the shape of the
water box gets deformed (somewhat octagonal)...Can anyone suggest what might
be the reason?. I have commented out the cellbasisvector in the
configuration file. The rmsd is also shooting up during equilibration. Below
is the configuration file that I used.
Any suggestion will be appreciated.

#Minimization and Equilibriation
set inputname try_heat
structure pro_wi.psf
coordinates pro_wi.pdb
#set temperature 310
set outputname pro_equi
bincoordinates $inputname.restart.coor
binvelocities $inputname.restart.vel
extendedSystem $inputname.restart.xsc

proc get_first_ts { xscfile } {
  set fd [open $xscfile r]
  gets $fd
  gets $fd
  gets $fd line
  set ts [lindex $line 0]
  close $fd
  return $ts

set currenttimestep [get_first_ts $inputname.restart.xsc]
#set currenttimestep 0

firsttimestep $currenttimestep

paraTypeCharmm on
parameters par_all22_prot_cmap.inp
#temperature $temperature

#Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12
switching on
switchdist 10
pairlistdist 14

#Integrator Parameters
timestep 2.0
rigidBonds all
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20

#Constant Temperature Control
langevin on
langevinDamping 5
langevinTemp 300
langevinHydrogen no

#periodic boundary conditions
#cellBasisVector1 110.56 00.00 00.00
#cellBasisVector2 00.00 129.55 00.00
#cellBasisVector3 00.00 00.00 213.95
cellOrigin 55.27 65.18 106.93
wrapWater on
wrapAll on
PME yes
PMEGridSizeX 120
PMEGridSizeY 135
PMEGridSizeZ 225

#Constant Pressure Control
useGroupPressure yes
useFlexibleCell yes
#useConstantArea yes
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp 300

OutputName $outputname
binaryoutput no
restartfreq 1000
dcdfreq 1000
outputEnergies 1000
outputPressure 1000
xstFreq 1000
binaryrestart yes

#Execution Script
#minimize 3500
#reinitvels $temperature

run 100000

Thanks and regards

Member Research Team
Lead Invent Technology
TBIU, IIT Delhi, India
Email- sunita_at_leadinvent.com
Ph- +9111 26581524 (Ex-6)

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