From: David Minh (daveminh_at_gmail.com)
Date: Fri Apr 20 2012 - 13:10:29 CDT
Hello again,
I worked it out! It was the fullElectFrequency 2 term. It should be fullElectFrequency 1. Let this be a warning to others to not skip timesteps when postprocessing...
David
On Apr 20, 2012, at 2:03 PM, David Minh wrote:
> Hello NAMD developers,
>
> I'm trying to do something like MM/PBSA using NAMD_2.9b3_Linux-x86_64-multicore. The problem is that the BOUNDARY energy term (from SASA) does not always appear when I postprocess the trajectory. It seems to flicker on and off (see bottom). Everything else seems reasonably consistent. Is there something wrong with my configuration file, or is this a bug with NAMD somewhere?
>
> Thanks,
> David
>
> This is my namd configuration file to generate the trajectory:
>
> ---
>
>
> # Variables
> set systemName cb7bcb
> set temperature 300
> set outputname $systemName\_sim
>
> # Input files
> structure ../1-build/$systemName.psf
> coordinates ../1-build/$systemName.pdb
> bincoordinates cb7bcb_therm.coor
>
>
> # Force field parameters
> paraTypeCharmm on
> parameters ../1-build/from_Yi/par_all36_cgenff_ywdp.prm
>
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchdist 15
> cutoff 16
> pairlistdist 17.5
>
> # Integrator parameters
> timestep 2.0
> rigidBonds all
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
> # Temperature control
> temperature $temperature
> langevin on
> langevinDamping 1
> langevinTemp $temperature
> langevinHydrogen off ;# Don't couple bath to hydrogens
>
> # Generalized Born/Surface Area parameters
> GBIS on
> ionConcentration 0.0 ;# "essentially pure water (Moghaddam et. al., 2011)"
> sasa on
> surfaceTension 0.005
>
> # Output parameters
> outputName $outputname
> binaryoutput yes
>
> restartfreq 1000000 ;# 1 ns
> dcdfreq 1000 ;# 2 ps
> outputEnergies 1000 ;# 2 ps
>
>
> # Execution
>
> reinitvels $temperature
> langevinTemp $temperature
> run 2500000 ;# 5 ns
>
> ---
>
> This is my namd configuration file to postprocess the simulation:
>
> ---
>
> # Variables
> set sysName cb7bcb
> set temperature 0
> set outputname $sysName\_pp
>
> # Input files
> structure ../1-build/$sysName.psf
> coordinates ../1-build/$sysName.pdb
>
> (the same as above between "Force Field Parameters" and "binaryoutput")
>
> # Execution
>
> set ts 0
> coorfile open dcd cb7bcb_sim.dcd
> while { ![coorfile read] } {
> firstTimestep $ts
> run 0
> incr ts 1
> }
> coorfile close
>
>
> ---
>
> Here are some relevant energy lines from the simulation output:
>
> ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
>
> ENERGY: 1000 36.0577 390.8935 81.6645 49.1624 -671.8579 -63.0646 1.1874 0.0000 118.8244 -57.1327 293.1135 -175.9571 -53.8906 311.3009
> ENERGY: 2000 40.7414 367.5730 80.2306 52.5194 -670.3409 -61.1538 1.6029 0.0000 120.2077 -68.6197 296.5258 -188.8273 -66.1092 285.9393
> ENERGY: 3000 42.3278 364.2220 80.2892 64.0130 -672.5005 -67.4494 1.1976 0.0000 119.6957 -68.2046 295.2627 -187.9003 -64.3559 289.6042
> ENERGY: 4000 39.6181 377.8628 79.1784 46.6799 -676.8757 -56.6396 1.4173 0.0000 119.1413 -69.6174 293.8953 -188.7587 -65.5157 297.2024
> ENERGY: 5000 33.5424 368.4974 81.3389 54.2557 -671.7889 -63.1159 1.6890 0.0000 100.0634 -95.5181 246.8342 -195.5814 -92.0752 297.2865
> ENERGY: 6000 39.1976 360.2947 79.5993 63.0037 -672.8300 -64.3088 1.0339 0.0000 117.7495 -76.2601 290.4620 -194.0096 -73.2671 282.3013
>
> Here are the relevant energy lines from the postprocessing:
>
> ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
>
> ENERGY: 0 36.0575 390.8934 81.6645 49.1624 -671.8579 -63.0646 1.1874 0.0000 0.0000 -175.9573 0.0000 -175.9573 -172.1641 0.0000
> ENERGY: 1 40.7413 367.5728 80.2306 52.5194 -670.3408 -61.1537 0.0000 0.0000 0.0000 -190.4305 0.0000 -190.4305 -186.3239 0.0000
> ENERGY: 2 42.3273 364.2217 80.2893 64.0129 -672.5005 -67.4495 1.1976 0.0000 0.0000 -187.9010 0.0000 -187.9010 -183.2057 0.0000
> ENERGY: 3 39.6178 377.8628 79.1784 46.6799 -676.8757 -56.6397 0.0000 0.0000 0.0000 -190.1765 0.0000 -190.1765 -185.4449 0.0000
> ENERGY: 4 33.5428 368.4970 81.3389 54.2557 -671.7890 -63.1159 1.6890 0.0000 0.0000 -195.5815 0.0000 -195.5815 -189.4797 0.0000
> ENERGY: 5 39.1976 360.2946 79.5994 63.0039 -672.8300 -64.3088 0.0000 0.0000 0.0000 -195.0434 0.0000 -195.0434 -190.1460 0.0000
>
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