From: Jorge Pikunic (jorge.pikunic_at_bioch.ox.ac.uk)
Date: Mon Jun 28 2004 - 16:23:14 CDT
Hello,
Does the tcl scripting interface work on NAMD 2.5 for IBM-SP? After
specifying all the variables, options, etc. in my NAMD configuration
file, I use "minimize 0" to go to scripting mode, and then use a
simulation protocol:
# turn Langevin piston off
minimize 0
langevinPiston off
# minimize non-protein atoms
minimize 3000
output min_fix
# minimize all atoms, a-C restrained
fixedAtoms off
minimize 3000
output min_all
# run with a-C restrained, heat to target temperature
langevin on
run 200000
output heat
# turn Langevin piston on, a-C still restrained
langevinpiston on
run 200000
output equil_ca
It runs on an Intel processor, but when I run it on an IBM-SP, I get the
following errors:
Info: Configuration file is equilibration.namd
ERROR: Multiple definitions of 'Langevin'
ERROR: in the configuration file are not allowed
ERROR: Multiple definitions of 'LangevinPiston'
ERROR: in the configuration file are not allowed
ERROR: Multiple definitions of 'fixedatoms'
ERROR: in the configuration file are not allowed
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: run
ERROR: output
ERROR: minimize
ERROR: set
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
Thank you in advance,
Jorge
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