restart a simulation

From: upayan baul (
Date: Thu Mar 15 2012 - 07:20:42 CDT

I am very new to using NAMD. I am trying to equilibrate a box of water in
steps. The first run works but I'm unable to restart it. Please point out
my mistake. I attach the error message in log file too.

The input files exist in the directory.


structure ../water/solvate.psf
coordinates ../water/solvate.pdb

set temperature 298
set outputname wb_eq2

# Continuing a job from the restart files
if {1} {
set inputname wb_eq1
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel
extendedSystem $inputname.restart.xsc

temperature $temperature
minimize 100
reinitvels $temperature


firsttimestep 200001

# Input
paraTypeCharmm on
parameters ../water/par_all27_prot_lipid.inp
temperature $temperature

# Force-Field Parameters
exclude 1-3
#1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0

# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 1fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
cellBasisVector1 48.0 0. 0.0
cellBasisVector2 0.0 25.0 0.0
cellBasisVector3 0.0 0 48.0
cellOrigin 23.90 12.51 23.99

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
#PMEGridSpacing 1.0

#manual grid definition
PMEGridSizeX 60
PMEGridSizeY 60
PMEGridSizeZ 60

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 500
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100

# Minimization
minimize 100
reinitvels $temperature

run 200000 ;

log file:
Charm++: standalone mode (not using charmrun)
Charm++> cpu topology info is being gathered.
Charm++> Running on 1 unique compute nodes (2-way SMP).
Info: NAMD 2.7b2 for Linux-x86
Info: Please visit
Info: and send feedback or bug reports to
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: Based on Charm++/Converse 60103 for net-linux-iccstatic
Info: Built Thu Nov 12 22:11:41 CST 2009 by jim on
Info: 1 NAMD 2.7b2 Linux-x86 1 as38 upayanb
Info: Running on 1 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 27360.5 s
Info: 1.22376 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is wb_eq.conf
TCL: Suspending until startup complete.
ERROR: 'cutoff' is a required configuration option
ERROR: cutoff defines: local electrostatic and Vdw distance
ERROR: 'exclude' is a required configuration option
ERROR: exclude defines: Electrostatic exclusion policy
ERROR: 'outputname' is a required configuration option
ERROR: outputname defines: prefix for the final PDB position and velocity
[0] Stack Traceback:
  [0] _ZN9NamdState14configListInitEP10ConfigList+0x369 [0x84aadcd]
  [1] _ZN9ScriptTcl9initcheckEv+0x54 [0x84fd338]

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