From: Mariana Graterol (marianagraterol_at_gmail.com)
Date: Tue Aug 28 2012 - 08:07:03 CDT
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!
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 *
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