pmf calculation

From: Christine Horejs (horejs_at_gmx.net)
Date: Tue Apr 17 2007 - 08:20:41 CDT

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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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