From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Sun Oct 08 2006 - 00:12:39 CDT
Hi all
when i am minimizing my protein in water box, i am getting zero
kinetic energy, zero temperature and zero boundary. what may be the reason
and how to solve this problem. my configuration file is
############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Sphere
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ../common/prodh_wb.psf
coordinates ../common/prodh_wb.pdb
set temperature 310
set outputname prodh1_min
if {0} {
set inputname prodh_min
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry
if you use this!
extendedSystem $inputname.xsc
}
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ../common/par_all27_prot_lipid.inp
temperature $temperature
# 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
# 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 -81.875 0. 0.
cellBasisVector2 0. -79.3840036392 0.
cellBasisVector3 0. 0 -81.5929965973
cellOrigin 5.72501993179 45.225315094 49.4890518188
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 82
PMEGridSizeY 80
PMEGridSizeZ 82
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 250
outputPressure 250
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#les off
#lesFactor 10
#lesReduceTemp on
#lesReduceMass on
#lesCol B
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 5000
#reinitvels $temperature
#run 500000 ;# 1000 ps
Thank you in advance for help.
-- Dhiraj Kumar Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153
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