Re: Re: Bug with BOUNDARY energy in postprocessing?

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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