Re: ABF Simulation

From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Wed Oct 05 2005 - 11:35:25 CDT

Dear Lionel,

This error message might indicate a bug, either in my code or in the Tcl
interpreter, or both :-/
Would it be a problem for you to provide me with the necessary files so that I
can reproduce the problem here? This would include the initial structure,
force field parameters, and the output of your existing simulation.

Thanks,
Jerome

On Wednesday 05 October 2005 13:41, Lionel Perrin wrote:
> Dear all,
>
> I am trying to run an ABF simulation, it has started well but has
> aborted after 247ps of simulation and got :
>
> TCL: ABF> Xi at timestep 247000 : 6.16169595314
> PRESSURE: 247000 169.299 88.5974 144.175 88.5974 -257.586 -103.904
> 144.175 -103.904 305.777
> GPRESSURE: 247000 397.897 61.4437 242.879 154.69 -7.13539 -62.5883
> 110.77 -313.301 402.161
> PRESSAVG: 247000 253.302 -27.9105 -38.5076 -27.9105 152.077 17.2412
> -38.5076 17.2412 219.491
> GPRESSAVG: 247000 253.81 -28.5958 -37.6107 -26.3772 154.377 17.3647
> -35.0004 19.1543 220.654
> ENERGY: 247000 1177.5016 1677.8484 1319.1461
> 0.0000 -88897.3370 9497.0819 0.0000
> 0.0000 15980.0225 -59245.7364 303.3274
> -59221.9021 -59226.4400 301.2477 72.4969
> 264.3078 246075.1769 208.2897 209.6137
>
> TCL: unknown floating-point error, errno
> = 22 FATAL ERROR: unknown floating-point error, errno = 22
> while executing
> "expr $retval + $term * $term"
> (procedure "veclength2" line 4)
> invoked from within
> "veclength2 $v"
> (procedure "veclength" line 2)
> invoked from within
> "veclength [vecsub $coords($abf2) $coords($abf1)"
> (in namespace eval "::ABF::ABFcoord" script line 4)
> invoked from within
> "namespace eval ABFcoord {
> loadcoords coords
>
> set r [veclength [vecsub $coords($abf2) $coords($abf1)]]
> return $r
> }"
> (procedure "ABFcoord" line 3)
> invoked from within
> "ABFcoord"
> (in namespace eval "::ABF" script line 52)
> invoked from within
> "namespace eval ::ABF {
>
> # First timestep : we don't have forces
> if { $timestep == 0 } {
>
> # must not be equal to $timestep - 1
> set timeStored -2
> ..."
> (procedure "calcforces" line 2)
> invoked from within
> "calcforces"
>
> Here is my NAMD input :
>
> outputName 1J8A_abf
>
> set temperature 300 set
> inputname 1J8A_abf binCoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel
> extendedSystem $inputname.restart.xsc
>
> firsttimestep 0 ##
> SIMULATION PARAMETERS amber yes parmfile
> 1J8Aprm.top
> ambercoor 1J8Aprm.crd
>
> # Periodic Boundary conditions
> wrapAll on
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 14.
> switching on
> switchdist 12.
> pairlistdist 16.
>
> # Integrator Parameters
> timestep 1.0
> rigidBonds water
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
> usesettle yes
>
> #PME PME
> yes
> PMEGridSizeX 64
> PMEGridSizeY 64
> PMEGridSizeZ 64
>
> # Constant Temperature
> Control langevin on
> langevinDamping 5
> langevinTemp $temperature
> langevinHydrogen yes
>
>
>
> restartfreq 2000 restartsave no
> dcdfreq 2000
> xstFreq 2000
> outputEnergies 1000
> outputPressure 1000
>
> ## ABF
>
> source /applx/NAMD_2.6b1_Linux-i686/lib/abf/abf.tcl
> abf coordinate distance
> abf abf1 2471
> abf abf2 3232
> abf ximin 3.0
> abf ximax 13.0
> abf dxi 0.1
> abf dsmooth 0.2
> abf fullsamples 500
> abf outfile 1J8A_abf.abf
> abf historyfile 1J8A_abf.his
> abf outputfreq 5000
> abf writexifreq 1000
> abf distfile 1J8A_abf.dis
>
> ## EXECUTION SCRIPT run
> 6000000
>
> Does anyone have a clue ? Am I doing something wrong ?
>
> all the best,
>
> thanks,
>
> Lionel

-- 
Jérôme Hénin
Equipe de Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS
Tel : (33) 3 83 68 43 95        Fax : (33) 3 83 68 43 87
http://www.edam.uhp-nancy.fr/

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