From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Jun 28 2010 - 20:23:43 CDT
Parisa,
Have you minimized your system and checked for atoms that are clashing, too
close to one another, perhaps even "on top of" each of? Your very high VDW
energy is usually indicative of such problems.
If you haven't already minimized, try that. If you have minimized,
achieving converging energies, then you should examine your system manually
for atoms in too-close of contact.
Best,
Chris
On Mon, Jun 28, 2010 at 1:47 PM, Parisa Akhski <
Parisa.Akhshi_at_chem.queensu.ca> wrote:
>
> 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
>
>
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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