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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