From: Ganesh Shahane (ganesh7shahane_at_gmail.com)
Date: Thu Apr 25 2013 - 08:51:59 CDT
Dear all,
My water box is getting deformed during the equilibration run. It turns
into a sphere in the first half and then into a rectangular slab-like
shaped box in the second half of equilibration. Anyone knows whats wrong?
Initially, the waterbox was created with a minimal distance of 15 angstrom
between any protein atom and the boundary of the box . Then stepwise
minimization was performed using CHARMM 36 programme. Then it was minimized
with 1000 steps of CG as implemented in NAMD and heated from 0 to 300 K.
Following are my equilibration parameters:-
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 # 2fs/step
rigidBonds all # needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
#Velocity reassginment
rescaleFreq 500
rescaleTemp 300
# Periodic Boundary Conditions
cellBasisVector1 115.82 0. 0.
cellBasisVector2 0. 115.46 0.
cellBasisVector3 0. 0. 77.98
cellOrigin 0 0 0
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 120
PMEGridSizeY 120
PMEGridSizeZ 90
#Constant pressure control
useGroupPressure yes
useFlexibleCell no
BerendsenPressure on
BerendsenPressureTarget 1
BerendsenPressureCompressibility 0.000049
BerendsenPressureRelaxationTime 500
BerendsenPressureFreq 20
# Output
binaryoutput yes
outputName $outputname
restartfreq 1000
dcdfreq 1000
xstFreq 1000
outputEnergies 1000
outputPressure 1000
-- Ganesh MSc Bioinformatics University of Pune.
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