From: uma mageshwari (mageshwariuma6_at_gmail.com)
Date: Wed Jan 28 2009 - 04:11:57 CST
Hai all
I am running a dynamics for protein-dna complex(nucleosome) in vacuum
2.I think i am in need of PBC eventhough i dont have solvent. Because in a
paper it is given that molecules will evaporate wen there is no boundary
conditions.Is it so?
3.Minimisation is ok.Energy is keep on decreasing. But in the case of
simulation there is sudden increase in the energy and generating numbers
99999999.99999. i dont know why?
I have included my configuration file also. have a look at this.
timestep 0.000000002 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 128. 0. 0.
cellBasisVector2 0. 199. 0.
cellBasisVector3 0. 0. 53.
cellOrigin 56. 100. 8.
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 110
PMEGridSizeY 180
PMEGridSizeZ 42
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
# Minimization
minimize 15000
reinitvels $temperature
run 10000 ;# 5ps
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