script for equilibration

From: matziast_at_med.uth.gr
Date: Sun Oct 02 2011 - 04:19:19 CDT

Hi,
I need your help. In the following script I want to ask you this: the last
command is minimize. Does this minimization follow the equilibration? Because I
would like to run after equilibration, a minimization. Is it the right script?
I would appreciate if anyone could help me.
Thank you in advance,
Maria.

#########################################
### JOB DESCRIPTION
#########################################
# Equilibration of run.coor
##############################################

## ADJUSTABLE PARAMETERS
##############################################

structure run.psf
coordinates run.pdb
#bincoordinates eq1.1.coor
set temperature 300
set outputname eq
firsttimestep 0

##############################################
## SIMULATION PARAMETERS
##############################################

# Input
paraTypeCharmm on
parameters run.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
#dielectric 80 ##########23/11/2010
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
# Output
outputName $outputname
restartfreq 500 # 500steps = every 1ps
dcdfreq 250
outputEnergies 100
outputPressure 100

###########################################
## EXTRA PARAMETERS
###########################################

# Spherical boundary conditions
#sphericalBC on
#sphericalBCcenter 22.04675205 62.204443 16.8283
#sphericalBCr1 62.5 # distance at which the first boundary potential begins to
act
#sphericalBCk1 10 # force constant for the harmonic bountary potential
#sphericalBCexp1 2

# Constraints and restraints
#fixedAtoms on
#fixedAtomsForces on
#fixedAtomsFile Y-0.ref
#fixedAtomsCol B
##########################################
## EXECUTION SCRIPT
##########################################

# Minimization
minimize 250
reinitvels $temperature;

run 500000; # 1 ns

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