From: Martin Loewer (m.loewer_at_cns.uni-frankfurt.de)
Date: Fri Apr 21 2006 - 05:50:28 CDT
Hello,
when starting a dynamics simulation, minimization runs well and it
always (tried serveral times) runs until setp 1000 and produces the
following error message (end of log file):
WRITING COORDINATES TO DCD FILE AT STEP 1000
WRITING COORDINATES TO RESTART FILE AT STEP 1000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 1000
FINISHED WRITING RESTART VELOCITIES
TCL: Setting parameter reassignFreq to 100
FATAL ERROR: Setting parameter reassignFreq from script failed!
Stack Traceback:
[0] CmiAbort+0x51 [0x734751]
[1] _Z8NAMD_diePKc+0x63 [0x49ab63]
[2] _ZN13SimParameters9scriptSetEPKcS1_+0x4be [0x66dea6]
[3] _ZN4Node11scriptParamEP14ScriptParamMsg+0x25 [0x617a25]
[4] _ZN12CkIndex_Node32_call_scriptParam_ScriptParamMsgEPvP4Node+0x12 [0x6179fa]
[5] CkDeliverMessageFree+0x30 [0x6cfe38]
[6] _Z15_processHandlerPvP11CkCoreState+0x44a [0x6d24ca]
[7] CmiHandleMessage+0x26 [0x73b1ae]
[8] CsdScheduleForever+0x4b [0x73b30b]
[9] CsdScheduler+0x1c [0x73c98c]
[10] _ZN7BackEnd7suspendEv+0xe [0x4a1536]
[11] _ZN7BackEnd7barrierEv+0xe [0x4a14fe]
[12] _ZN9ScriptTcl12setParameterEPKcS1_+0x137 [0x657a27]
[13] _ZN9ScriptTcl9Tcl_paramEPvP10Tcl_InterpiPPc+0x18c [0x65697c]
[14] TclInvokeStringCommand+0x91 [0x758d78]
[15] /home/loewer/bin/NAMD/namd2 [0x78ebc8]
[16] /home/loewer/bin/NAMD/namd2 [0x78e9e1]
[17] Tcl_EvalEx+0x176 [0x78f20b]
[18] Tcl_EvalFile+0x134 [0x786c14]
[19] _ZN9ScriptTcl3runEPc+0x1c [0x656294]
[20] main+0x222 [0x49dae2]
[21] __libc_start_main+0xda [0x2aaaab12a5aa]
[22] _ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_c+0x5a [0x49a4aa]
This looks like a bug in the program to me. Maybe I can change my config
file (see below) to avoid this.
Sincerly,
Martin Loewer
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure sp_wb.psf
coordinates sp_wb.pdb
set temperature 310
set outputname sp_wb_eq
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.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 82. 0. 0.
cellBasisVector2 0. 90. 0.
cellBasisVector3 0. 0 90.
cellOrigin 29.0915279388 -18.3676776886 17.4208488464
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 96
PMEGridSizeY 96
PMEGridSizeZ 96
# 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 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 1000
## Heating Process
reassignFreq 100
reassignTemp 31
reassignIncr 31
reassignHold $temperature
reinitvels 31
run 3500 ;# 7ps
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