From: David Minh (daveminh_at_gmail.com)
Date: Tue Apr 10 2012 - 08:35:37 CDT
Thanks JC!
On Apr 9, 2012, at 7:27 PM, JC Gumbart wrote:
> 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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