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From: Peter Mawanga (peter.mawanga.lagos_at_gmail.com)
Date: Wed May 23 2018 - 08:42:05 CDT

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Greetings to everyone

I calculated the non-bonded interactions (VdW and Electrostatic) between
two selections, using the same "cutoff" and "switch" distance as employed
in simulations:

============================================================================

namdenergy -vdw -elec -nonb -sel [atomselect top "segname AP1"] [atomselect
top "segname AP2"] -exe ../namd2 -extsys relaxation/equil_out.xsc -T 310
-switch 9 -cutoff 12 -pme -par ../martini-protein-bonds.par -par
./martini-protein-angles-cos.par -par ../martini-protein-dihedrals.par
-par ../martini-all-nonb.par -ofile "nonb_pep.dat"

============================================================================

However, when I tried to calculate the interaction energy within the
system:

============================================================================

namdenergy -elec -sel [atomselect top all] -exe ../namd2 -extsys
relaxation/equil_out.xsc -T 310 -switch 9 -cutoff 12 -pme -par
./martini-protein-bonds.par -par ../martini-protein-angles-cos.par -par
./martini-protein-dihedrals.par -par ../martini-all-nonb.par -ofile
"nonb_sys.dat"

============================================================================

I got the following error:

============================================================================

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Low global exclusion count! (266 vs 268) System
unstable or pairlistdist or cutoff too small.

FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html

Charm++ fatal error:
FATAL ERROR: Low global exclusion count! (266 vs 268) System unstable or
pairlistdist or cutoff too small.

FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html

============================================================================

Any insight regarding this error would be highly appreciated.