From: David Minh (daveminh_at_gmail.com)
Date: Mon Apr 09 2012 - 12:36:25 CDT
Hello NAMD users/developers,
I am getting a strange result with NAMD 2.9b3 for Linux-x86_64-multicore: a non-zero BOUNDARY energy term even without periodic boundary conditions or restraints of any sort. Here is an energy from the early in my simulation.
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
ENERGY: 10000 6.9586 14.5069 3.4136 0.0000 -2299.1275 -18.2221 38.7778 0.0000 15.2441 -2238.4486 319.6335 -2253.6928 -2237.9923 302.3148
Below is the input file. There are no periodic boundaries and I even turned off rigidbonds. What could be causing the 38.7778 kcal/mol?
David
set temperature 300
set outputname sim_apIND
amber on
parmfile ../1-build/apIND.prmtop
ambercoor ../1-build/apIND.crd
bincoordinates mintherm_apIND.restart.coor
### Force Field Parameters
exclude scaled1-4
1-4scaling 0.833333
# Generalized Born
GBIS on
ionConcentration 0.05
alphaCutoff 14
# Nonbonded
switching on
switchdist 15
cutoff 16
pairlistdist 18
# Hydrophobic
sasa on
surfaceTension 0.005
timestep 1
fixedAtoms on
fixedAtomsFile ../1-build/apIND_fix.pdb
fixedAtomsCol O
temperature $temperature
rigidBonds none
langevin on
langevinDamping 1
langevinTemp $temperature
langevinHydrogen off
outputName $outputname
binaryoutput yes
restartfreq 100000
dcdfreq 1000
outputEnergies 1000
reinitvels $temperature
langevinTemp $temperature
run 1000000
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