From: Lionel Perrin (lionel.perrin_at_cea.fr)
Date: Wed Oct 05 2005 - 06:41:44 CDT
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
-- !------------------------------------------! Lionel PERRIN Chargé de Recherche au CNRS DSV/DBJC/SBFM, URA 2096 du CNRS CEA-Saclay, build. 528, office #215 tel : (+33) (-0)1 69 08 96 81 fax : (+33) (-0)1 69 08 40 07 91191 Gif-sur-Yvette Cedex France !------------------------------------------!
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