From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Mon Jun 28 2010 - 13:47:39 CDT
Dear Jerome and all NAMD users,
I am trying to calculate PMF profile using ABF method for an ion transition process through the channel. The problem is that NAMD crashes at the start of the job with the message below:
TCL: Running for 5000000 steps
TCL: ABF> Data written to output files at timestep 0
PRESSURE: 0 NaN NaN NaN NaN NaN NaN NaN NaN NaN
GPRESSURE: 0 NaN NaN NaN NaN NaN NaN NaN NaN NaN
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 582.4585 1045.6107 821.0416 1.5227 -15383.8557 1761940.8175 0.0000 0.0000 NaN NaN NaN 1749007.5954 NaN NaN NaN NaN 60219.7200 NaN NaN
OPENING EXTENDED SYSTEM TRAJECTORY FILE
Does anyone know what the problem could be?
This is the configuration file:
########################################################
## Input files
structure dna_wb.psf
coordinates dna_wb.pdb
########################################################
## Output files
set job dna
outputName $job
restartname $job
########################################################
## Force field
paraTypeCharmm on
parameters par_all27_na.prm
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5
margin 3.0
########################################################
# Periodic Boundary Conditions
wrapAll on
cellBasisVector1 36.0 0. 0.
cellBasisVector2 0. 40.7 0.
cellBasisVector3 0. 0. 41.1
cellOrigin 0. 0. 0.
PME yes
PMEGridSizeX 36
PMEGridSizeY 40
PMEGridSizeZ 40
########################################################
## Ensemble
set temperature 298.15
temperature $temperature
COMmotion no
timestep 1.0
rigidBonds all
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 20 ;# nonbond list updated every 20 steps
## Constant temperature
tCouple on
tCoupleTemp $temperature
## Constant pressure
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
########################################################
# Output
restartfreq 10000 ;# = every 1ps
dcdfreq 1000
xstFreq 10000
outputEnergies 10000
outputPressure 10000
########################################################
## Extra simulation parameters
# ABF SECTION
source /opt/namd/2.6/32bit/lib/init.tcl
package require abf
abf coordinate zCoord
abf abf2 { 781 }
abf abf1 { 89 284 479 674 122 707 317 512 }
abf dxi 0.2
abf xiMin -10.0
abf xiMax 10.0
abf forceConst 10.0
abf outFile dna.dat
abf fullSamples 500
abf distFile dna.dist
abf dSmooth 0.4
abf applyBias yes
abf historyFile dna.history
run 5000000
Thanks in advance for your help,
Parisa
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