From: Norman Geist (norman.geist_at_uni-greifswald.de)
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 didn’t 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, that’s nonsense. Also it’s nonsense to
load a velocity file, and then minimize as all velocities get lost then,
there’s no need to minimize every run you restart, it’s 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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von upayan baul
Gesendet: Donnerstag, 15. März 2012 13:21
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: restart a simulation
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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