problem in running targeted MD

From: giulia palermo (
Date: Wed Feb 24 2016 - 19:56:11 CST

Dear all,

I am running targeted MD simulations using NAMD.
Do to so, I have created a reference PDB file (the target) containing the
exact atoms (including type, name, serial number, etc. ..) of the
structure that I want to target. Importantly, this PDB file does not
contain water molecules, but only the protein atoms. Moreover, in the
reference PDB, the occupancy (not the beta factor) of all heavy atoms has
been set to a non zero value (i.e., 200).

After having equilibrated the system, I have created the TMD input file, in
which I specify the essential parameters.
The input contemplates langevin dynamics, as suggested in the manual.
However, the simualtion crashes with the following error:

Charm++ fatal error:

Based on the attached input file, could you please help me in understanding
what is the fatal error that leads my simulation crashing?

Thank you very much

My input file is the following.
# Input
#paraTypeCharmm off
amber on
parmfile SYS.prmtop
ambercoor SYS.crd
readexclusions on # exclusions are taken from the prmtop made by leap

# Restart Options
extendedSystem SYS_MD_NPT300.xsc
bincoordinates SYS_MD_NPT300.coor
binvelocities SYS_MD_NPT300.vel
restartname SYS_PROD.restart

# Force-Field Parameters (File di M.Stenta)
exclude scaled1-4
1-4scaling 0.833333 # =1/1.2, default is 1.0
cutoff 12.
switching off
#switchdist 10.
pairlistdist 13.5

# Minimizator Parameters
minimization off
minLineGoal 1.0e-4

# Integrator Parameters (File di M.Stenta)
timestep 2.0 # 2fs/step
rigidBonds all # needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
firsttimestep 0

# Constant Temperature Control
langevin on # do langevin dynamics
langevinDamping 5 # damping coefficient (gamma) of 5/ps
langevinTemp 300
langevinHydrogen off # don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
cellbasisvector1 136.218 0.000 0.000
cellbasisvector2 0.000 103.626 0.000
cellbasisvector3 0.000 0.000 147.488
cellorigin 68.109 51.813 73.744
wrapAll on # allows translation of coordinates whether objects
cross periodic boudaries
COMmotion off # disable initial center of mass motion

# PME (for full-system periodic electrostatics) (File di M.Stenta)
PME yes
PMEGridSpacing 1.0

# Constant Pressure Control (variable volume)
useGroupPressure yes # needed for rigidBonds
useFlexibleCell no # isotropic dimensions rescaling if disabled
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 # in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp 300

# Output
outputName SYS_PROD
XSTfile SYS_PROD.xst

# Output optimized for MD (valori G.Palermo mantenuti perche' lo scaling
plot e' stato fatto cosi')
restartfreq 5000
dcdfreq 5000
xstFreq 5000
outputEnergies 500
outputPressure 500
outputMomenta 500

# Output optimized for EM
#restartfreq 500
#dcdfreq 100
#xstFreq 100
#outputEnergies 50
#outputPressure 50

# Run Control
# Minimization
#numsteps 500 # em01 protein constrained
#numsteps 1000 # em02

# Dynamics
numsteps 5000000 # 10ns for NPT equi at 300 K free

# Constraints
#fixedAtoms off
#fixedAtomsFile EM_CONST.pdb
#fixedAtomsCol B

# Restraints
binaryoutput yes # highest accuracy for the next run
binaryrestart yes # provides a pdb for further restraints
##constraints on
#consexp 2
#consref SYS_MD_TERM.pdb
#conskfile SYS_MD_TERM.pdb
#conskcol B
#Targeted MD
TMD on
TMDk 200
TMDOutputFreq 5000
TMDFile sys_target_occ.pdb
TMDFirstStep 0
TMDLastStep 5000000
TMDInitialRMSD from coordinates





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