From: twshen (tshen_at_uh.edu)
Date: Thu Jul 16 2009 - 12:04:03 CDT
Dear all,
I found that I reassign the temperature, in other words,
velocities, every 500 steps during the production run.
Since "reassignTemp" should be turned off during the
production run, I am wondering if this can make a
difference in the trajectory. Thank you very much.
Here are my simulation parameters for the production run,
# Input
paraTypeCharmm on
parameters toppar/par_all27_prot_na.prm
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.0
margin 2.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1 ;# nonbonded forces calculated every step
fullElectFrequency 1 ;# elect (PME) calculated every step
stepspercycle 10
# Reassign velocities
reassignFreq 500
reassignTemp 310
# Periodic Boundary Conditions (PBC) (cellorigin = center of the cell)
cellBasisVector1 107.00 0.0 0.0
cellBasisVector2 0.0 98.0 0.0
cellBasisVector3 0.0 0.0 94.0
cellOrigin 0.0 0.0 0.0
wrapWater on
wrapAll on
wrapNearest on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 120
PMEGridSizeY 100
PMEGridSizeZ 96
# Constant Pressure and Temperature Control (variable volume)
tCouple on
tCoupleTemp 310
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
BerendsenPressure on
BerendsenPressureTarget 1.01
BerendsenPressureCompressibility 0.000049
BerendsenPressureRelaxationTime 500
BerendsenPressureFreq 20
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