PMF force restraint question

From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Mon Jun 27 2005 - 19:11:11 CDT

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Hello!!

I want to change one dihedral angle of my protein slowly during a MD
simulation. I read in FreeEnergy calculations that can be achieved
throught a Force Restraint. My script :

structure ./wb-ionized.psf
coordinates ./wb-ionized.pdb

set outputname pmf
temperature 310
seed 986986
firsttimestep 0 ;# Last step previous run

paraTypeCharmm on
parameters /home/RPMs/NAMD/toppar/par_all22_prot.inp
exclude scaled1-4
1-4scaling 1.0
switching on

switchdist 8.; # cutoff-2
cutoff 10.; # may be 10 with PME
pairlistdist 12.; # cutoff+2
margin 0;

# Integrator Parameters
timestep 2.0; # 2fs/step
rigidBonds all; # needed for 2fs steps (SHAKE)
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 5
outputPairlists 1000

# Periodic Boundary Conditions
cellBasisVector1 53.40 0. 0.
cellBasisVector2 0. 55.33 0.
cellBasisVector3 0. 0. 41.38
cellOrigin -3.35 21.04 6.67

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 54
PMEGridSizeY 60
PMEGridSizeZ 45

# Constant Temperature Control
langevin on; # do langevin dynamics
langevinDamping 5; # damping coefficient (gamma) of 5/ps
langevinTemp 310
langevinHydrogen off; # don't couple langevin bath to hydrogens

# Output
outputName $outputname
binaryOutput no;

restartfreq 500; # 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100
outputTiming 1000

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

# FIXED ATOMS
fixedAtoms on
fixedAtomsForces on
fixedAtomsCol O; # If Ocupancy column=0.00 then that atom isn't fixed

#Free Energy
freeEnergy on
freeEnergyConfig {
        urestraint{
                dihe pmf (PROT,27,ca) (PROT,27,n)(PROT,27,o)(PROT,27,c) barr
= 500, low =179.02 , hi = 0.0
        }

        pmf {
                task = up
                time = 500 ps
                print = 10 ps
        }
}

# Minimization of the system: Protein fixed,waters free
minimize 100

# Relaxation of waters: Protein fixed,waters free
run 1000

# Minimization of the system: Protein fixed,waters free
minimize 100

# Minimization of the system: Protein and water free
fixedatoms off
minimize 200

reinitvels 310
run 250000

With such a config, NAMD give me this error:

Info: FREE ENERGY PERTURBATION CONFIG
Info: ***********************************

        urestraint{
                dihe pmf (PROT,27,ca)
(PROT,27,n)(PROT,27,o)(PROT,27,c) barr = 500, low =179.02 , hi = 0.0
        }

        pmf {
                task = up
                time = 500 ps
                print = 10 ps
        }

Info: ***********************************
FreeEnergy: Not enough steps to complete pfm & mcti blocks
FreeEnergy: Num Steps Needed = 250001
FreeEnergy: Num Steps Requested = 0
FATAL ERROR: FreeEnergy: Fatal Run-Time Error
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: FreeEnergy: Fatal Run-Time Error

I only add FreeEnergy values to a preexisting .conf of a NVT dynamics.
I am really lost, I dont know If I have to put dynamics controls as
run or minimize, or even where the error is. I thought this is like a
common MD but with a restraint, so could I set a simulation
temperature too??

Any help would be useful

Thanks a lot

Leonardo
Universidad de Chile
Undergraduate student
Biochemistry

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