From: upayan baul (margheritan22_at_gmail.com)
Date: Thu Mar 15 2012 - 07:20:42 CDT
Hi,
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.
Rehards,
Upayan
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:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60103 for net-linux-iccstatic
Info: Built Thu Nov 12 22:11:41 CST 2009 by jim on kyoto.ks.uiuc.edu
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
filenames
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
[0] Stack Traceback:
[0] _ZN9NamdState14configListInitEP10ConfigList+0x369 [0x84aadcd]
[1] _ZN9ScriptTcl9initcheckEv+0x54 [0x84fd338]
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