From: Adrian (adpala_at_hotmail.com)
Date: Tue Jul 23 2013 - 09:51:53 CDT
I'm trying to run "FullDirect yes" simulations, but I keep having an
error message saying:
------------- Processor 6 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Communicate::sendMessage not from Pe 0
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
after introducing the command
charmrun +p8 namd2 +idlepoll min1AML_Na15.namd > min1AML_Na15.log
What should I do to fix this, or how may I run a Full Direct
Electrostatics simulation to compare my ideal parameters for a simulation?
Thanks for all!
Adrian Palacios
If you want to see the config. file here it is:
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization of 1AML_Na15
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure 1AML_Na15.psf
coordinates 1AML_Na15.pdb
outputname min1AML_Na15
set temperature 298
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters
/usr/local/lib/vmd/plugins/noarch/tcl/readcharmmpar1.2/par_all27_prot_lipid_na.inp
temperature $temperature
# Periodic Boundary conditions
cellBasisVector1 100.84 0 0
cellBasisVector2 0 85.13 0
cellBasisVector3 0 0 83.82
cellOrigin 0 0 0
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12
switching off
pairlistdist 16
# Integrator Parameters
timestep 1.0
rigidBonds water
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
restartfreq 2000
dcdfreq 100
xstFreq 100
outputEnergies 200
#############################################################################
## EXTRA PARAMETERS ##
#############################################################################
binaryoutput no
binaryrestart no
#must of the missing parameters compared to previous minimizations
#were already defaults.
# Tested parameter
FullDirect yes
#############################################################
## EXECUTION SCRIPT ##
#############################################################
minimize 1000
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