(no subject)

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.

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:08 CST