From: Christine Horejs (horejs_at_gmx.net)
Date: Tue Apr 17 2007 - 08:20:41 CDT
Hi!
I have problems to integrate the pmf calculation in the config file; this is my config file:
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Sphere
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure sbsb.psf
coordinates sbsb.pdb
set temperature 300
set outputname sbsb_pmf
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters 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
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
freeEnergy on
freeEnergyConfig {
urestraint {
dist pmf group { (met, 1) to (met, 20) }
group { (asn, 222) to (lys, 913) } kf=20, low=20.0, hi=10.0
}
pmf {
task = grow
time = 10 ps
print = 1ps
}
pmf {
task = up
time = 100 ps
}
pmf {
task = stop
time = 10 ps
}
pmf {
task = down
time = 100 ps
}
mcti{
task = stepup
equiltime = 10ps
accumtime = 10ps
numsteps = 5
print = 1ps
}
mcti{
task = stepdown
}
}
################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 1000
reinitvels $temperature
run 25000 ;# 50ps
I can't find the mistake! Maybe anyone can help me?
Would be great!
Thank you and greetings from sunny Vienna,
Christine
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