From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Apr 09 2012 - 18:27:33 CDT
Hey David,
Looking at the NAMD source code, I find that it comes from the hydrophobic surface term of the implicit solvent. Specifically,
ComputeLCPO.C: reduction->item(REDUCTION_BC_ENERGY) += totalSurfaceArea * surfTen;
JC
On Apr 9, 2012, at 12:36 PM, David Minh wrote:
> 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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