From: bharat gupta (bharat.85.monu_at_gmail.com)
Date: Sun Jul 03 2011 - 20:36:19 CDT
Hi,
I want to know that the following parameters are for npt or nvt
equilibration :-
dielectric 1.0
coordinates ../common/complex_ionized.pdb
outputEnergies 1000
binaryoutput no
DCDFreq 1000
restartFreq 1000
binCoordinates ./complex_min.restart.coor
binaryrestart yes
structure ../common/complex_ionized.psf
paraTypeCharmm on
parameters ../common/par_all27_prot_na.prm
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
margin 2.0
stepspercycle 20
extendedSystem ./complex_min.xsc
outputname equilibrated
# Periodic Boundary Conditions
#cellBasisVector1 62.6 0.0 0.0
#cellBasisVector2 0.0 52.0 0.0
#cellBasisVector3 0.0 0.0 46.6
#cellOrigin 8.35 69.64 -10.16
berendsenPressure on
berendsenPressureTarget 1.01325 # atmospheric pressure
berendsenPressureCompressibility 4.57e-5 # liquid water
berendsenPressureRelaxationTime 100.0
berendsenPressureFreq 10
temperature 0.5 # starting at 0.5 K
reassignFreq 100
reassignIncr 0.5
reassignHold 300 # target T: 300 K
numsteps 100000
If its for npt, what changes are needed to make it for nvt or vice versa??
-- Bharat Ph.D. Candidate
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