From: 张鋆 (coolrainbow_at_yahoo.cn)
Date: Fri Apr 16 2010 - 22:04:17 CDT
Hi everyone!
I am performing the "Charging a spherical ion" exercise in the "A Tutorial on Alchemical Free Energy Perturbation Calculations in NAMD ", I have performed the exercise step by step with the tutorial, but my md died with:
TCL: Running for 25000 steps
FEP: RESETTING FOR NEW FEP WINDOW LAMBDA SET TO 0 LAMBDA2 0.0625
FEP: WINDOW TO HAVE 5000 STEPS OF EQUILIBRATION PRIOR TO FEP DATA COLLECTION.
FEP: USING CONSTANT TEMPERATURE OF 298 K FOR FEP CALCULATION
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 30.6528 74.5554 76.2156 0.0000 -25218.8767 9999999999.9999 0.0000 0.0000 nan nan nan 9999999999.9999 nan nan nan nan 27000.0000 nan nan
OPENING FEP ENERGY OUTPUT FILE
OPENING EXTENDED SYSTEM TRAJECTORY FILE
[2] Stack Traceback:
[0] /lib/libc.so.6 [0x7f0fa172bf60]
[1] _ZN12PmeRealSpace12fill_chargesEPPdPcS2_P11PmeParticle+0x901 [0x8f6731]
[2] _ZN10ComputePme6doWorkEv+0x103f [0x715f0f]
[3] _ZN11WorkDistrib18messageEnqueueWorkEP7Compute+0xb2 [0x950852]
[4] _ZN7Compute10patchReadyEiii+0x87 [0x4f3867]
[5] _ZN5Patch14positionsReadyEi+0x410 [0x8dfef0]
[6] _ZN9HomePatch14positionsReadyEi+0x111a [0x86517a]
[7] _ZN9Sequencer17runComputeObjectsEii+0xbe [0x9288de]
[8] _ZN9Sequencer9integrateEv+0xc7b [0x92372b]
[9] _ZN9Sequencer9threadRunEPS_+0x2ef [0x92f3ff]
[10] CthStartThread+0x20 [0x9cff60]
[11] /lib/libc.so.6 [0x7f0fa173d7c0]
I guess this is due to the infinite energy ( SOD NA0 overlapping), my conf file is :
#############################################################
## JOB DESCRIPTION ##
#############################################################
# FEP
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ./char.psf
coordinates ./char.pdb
set temperature 298
set outputname char
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ./par_all22_prot.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 30. 0. 0.
cellBasisVector2 0. 30. 0.
cellBasisVector3 0. 0. 30.
cellOrigin 25.7867336273 -20.6125450134 -12.3257799149
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 32
PMEGridSizeY 32
PMEGridSizeZ 32
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 5000 ;# 500steps = every 1ps
dcdfreq 2500
xstFreq 2500
outputEnergies 1000
outputPressure 1000
##########################################################
fixedAtoms on
fixedAtomsFile char.fep
fixedAtomsCol B
#############################################################
## FEP PARAMETERS ##
#############################################################
source ./fep.tcl
alch on
alchtype fep
alchFile char.fep
alchCol B
alchOutFile alchemy.alchOutFile
alchOutFreq 10
alchEquilSteps 1000
set nSteps 11000
set dLambda 0.1
runFEP 0.0 1.0 $dLambda $nSteps
the head of my char.fep is :
REMARK original generated coordinate pdb file
ATOM 1 SOD SOD 1 0.000 0.000 0.000 1.00 1.00 NA0
ATOM 2 NA0 NA0 2 0.000 0.000 0.000 1.00 -1.00 NA0
ATOM 3 OH2 TIP3 3 -17.244 23.344 -26.144 1.00 0.00 WT1 O
ATOM 4 H1 TIP3 3 -17.473 23.366 -25.167 1.00 0.00 WT1 H
ATOM 5 H2 TIP3 3 -17.961 23.747 -26.546 1.00 0.00 WT1 H
the psf was generated by alchemify. NAMD is 2.7b2
Can anyone give some ideas? Have I done something stupid? Thank you in advance. I can provide anything detail.
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