FullDirect Electrostatics

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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