AW: problem in running targeted MD

From: Norman Geist (
Date: Thu Feb 25 2016 - 01:38:33 CST




I’m quite sure that NAMD gave you more information why it stopped than just:


Charm++ fatal error:


Please check the output more carefully, as I already wonder that you use both “extendedsystem” and “cellbasisvector[1-3]”, NAMD will do so too.


Norman Geist


Von: [] Im Auftrag von giulia palermo
Gesendet: Donnerstag, 25. Februar 2016 02:56
Betreff: namd-l: problem in running targeted MD


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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