AW: restart a simulation

From: Norman Geist (
Date: Fri Mar 16 2012 - 02:01:34 CDT

Hi Upayan,


Remove the minimize command from the if clause. Namd will suddenly execute
the minimize command as it reads it, but you didnít set all needed
parameters till there. You also already set the minimize at the end of the
script. I think namd will then also complain about setting the temperature
AND reading velocities from restart, thatís nonsense. Also itís nonsense to
load a velocity file, and then minimize as all velocities get lost then,
thereís no need to minimize every run you restart, itís only for the initial
structure to find the energy minimum and if the initial structure has bad
contacts/bonds/angles etc.


Feel free to ask


Norman Geist.


Von: [] Im Auftrag
von upayan baul
Gesendet: Donnerstag, 15. Mšrz 2012 13:21
Betreff: namd-l: restart a simulation



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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