From: Claw Isthelaw (clawisthelaw_at_hotmail.com)
Date: Thu Jun 26 2008 - 10:41:53 CDT
Dear NAMD Community,
I'm trying to equilibrate a solvated protein using periodic boundaries. I cannot spot the error in the config file, but it keeps crashing with:
------------ Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
Charm++ fatal error:
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
Abort trap
The config file is below. Most of it seems fine, since I've been using that format to minimize proteins. However, whenever I set the DYNAMICS OUTPUT and/or the EQUILIBRATION switch(es) to 1 (on), it crashes with the above error. So I think the error is inside the DYNAMICS OUTPUT section. Does anyone see anything obvious?
Thanks,
Jeff Tibbitt
#################
# NAMD Input File
#################
# FILES
structure titin_ustate_box.psf
coordinates titin_ustate_box_min.pdb
outputname titin_ustate_box_equi
binaryoutput on
paraTypeCharmm on
parameters $env(TOPPAR)/par_all27_prot_na.prm
temperature 58
# FORCE FIELD
if {1} {
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 13.5
margin 0.0
stepspercycle 10
}
# PERIODIC BOUNDARY CONDITIONS
if {1} {
cellBasisVector1 177.43800354 0 0
cellBasisVector3 0 111.849998474 0
cellBasisVector2 0 0 234.277000428
cellOrigin 29.0831623077 -14.7965936661 88.4502029419
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
}
# CONSTRAINTS
if {1} {
constraints on
consref titin_ustate_box_min.pdb
conskfile titin_ustate_box_min.pdb
conskcol O
constraintScaling 0.95
}
# DYNAMICS PARAMETERS
if {1} {
timestep 2.0
rigidBonds all
outputEnergies 20
}
# DYNAMICS OUTPUT
if {1} {
restartname titin_ustate_box_equi
restartfreq 50
binaryrestart yes
DCDfreq 100
DCDfile titin_ustate_box_equi.dcd
outputEnergies 100
outputPressure 100
}
# EQUILIBRATION (OR SIMULATED ANNEALING) DYNAMICS EXECUTION
if {0} {
reassignFreq 100
for { set TEMP 58 } { $TEMP <= 298 } { incr TEMP 30 } {
reassignTemp $TEMP
run 100
}
}
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