ABF Simulation

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 

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 Lionel PERRIN
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