Bug with BOUNDARY energy in postprocessing?

From: David Minh (daveminh_at_gmail.com)
Date: Fri Apr 20 2012 - 13:03:31 CDT

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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