Problem with Targeted molecular dynamics

From: Agostino Bruno (
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:

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

set outputname *.

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 on
TMDk 100
TMDOutputFreq 100
TMDFile /*.pdb
TMDFirstStep 100000
TMDLastStep 4000000

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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