Problem with Targeted molecular dynamics

From: Agostino Bruno (agostino.bruno_at_nemo.unipr.it)
Date: Sun Feb 28 2010 - 10:07:25 CST

Dear all,
I'm trying to make a TMD simulation with NAMD2.6 version, but after 2ns this
message appear 'Bad Global Exclusion Count', in fact the protein it was
unfolded, so I tryied to change the TMDk from 200 to 100, and I launched an
other TMD simulation, but the current RMSD is not able to follow the target
RMSD, furthermore the protein becomes misfolded. In the NAMD mailing list I
read that there is a TMDŽbug in NAMDŽmpi version, Targeted Molecular Dynamics
works well in serial versions of NAMD, with a nice linear decrease of the
RMSD. With exactly the same parameters, the evolution of the RMSD is totally
different with a mpi version of NAMD. I'm using the NAMD2.6 version on a
cluster workstation with 24 processor and my configuration file as follows:

#Input
parmfile /*.prmtop
coordinates /*.pdb
bincoordinates /*.coor
binvelocities /*.vel
extendedSystem /*.xsc

set outputname *.

#Parameters
paraTypeCharmm off
amber on

set temperature 310
timestep 1.0
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
firsttimestep 0

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 10.
switching on
switchdist 8.
pairlistdist 12.

# Periodic Boundary Conditions
cellbasisvector1 85.370 0.000 0.000
cellbasisvector2 0.000 82.639 0.000
cellbasisvector3 0.000 0.000 76.137
cellorigin 0.061 -0.065 -0.337
wrapAll on
COMmotion off

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 128
PMEGridSizeY 128
PMEGridSizeZ 128

# Output
outputName $outputname
DCDfile *.dcd
DCDfreq 2000
xstFreq 2000
outputEnergies 4000
binaryrestart yes
restartname *.restart
restartfreq 2000

# Constant Temperature control
langevin on
langevinTemp $temperature
langevinDamping 1.

#Pressure control
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp $temperature

#TMD
TMD on
TMDk 100
TMDOutputFreq 100
TMDFile /*.pdb
TMDFirstStep 100000
TMDLastStep 4000000
TMDFinalRMSD 0

run 4500000

I would like know if NAMD2.7 is better than NAMD2.6 for my case, or if it is
possible to correct the bug in some way....

Thank you very much

--
Agostino Bruno
PhD Student
Dipartimento Farmceutico
Universita' degli Studi di Parma

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