help with the equilibration script

From: matziast_at_med.uth.gr
Date: Tue Dec 28 2010 - 16:31:44 CST

Hi, I encountered a problem with my simulation and I would appreciate if anyone
could me help me. I run the simulation on Windows Vista and when I type the
command to start the equilibration I get the message: incorrect atom count in
binary file ...restart.coor. I searched the messages at mailing list and
according to the replies I changed the script and in bincoordinates I have the
restart.coo.old file now but I get the same message. I send uoy the script to
tell me if you can what I have wrong.
#########################################
### JOB DESCRIPTION
#########################################

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

binaryrestart no
structure .psf
Coordinates .coor
bincoordinates .restart.coor
set temperature 300
set outputname ...
firsttimestep 0

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

# Input
paraTypeCharmm on
parameters par.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

# Output
outputName $outputname
restartfreq 500 # 500steps = every 1ps
dcdfreq 500
outputEnergies 100
outputPressure 100

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

# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 84.148 -43.258 -101.569
sphericalBCr1 138.0 # 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 .ref
fixedAtomsCol B

##########################################
## EXECUTION SCRIPT
##########################################

# Minimization
#minimize 100
reinitvels $temperature;

run 5000; # 10 ps

Should I omit the binaryrestart no?
I read the sample.conf but I do not understand which file is with the input
name.
Thank you very much in advance.
Happy new year!!!!!!!!!!!

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