From: Chris Harrison (charris5_at_gmail.com)
Date: Fri Apr 20 2012 - 19:41:37 CDT
David,
Do I correctly understand that your BOUNDARY energy actually is being
reported periodically as 0.000 in your log file, with periodicity
proportional to fullElectFrequency? I'm unclear what you mean by
"...when postprocessing."
Best,
Chris
On Fri, Apr 20, 2012 at 1:10 PM, David Minh <daveminh_at_gmail.com> wrote:
> 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
>>
>
>
-- Chris Harrison, Ph.D. NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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