From: Ravinder Abrol (abrol_at_wag.caltech.edu)
Date: Wed Dec 06 2006 - 18:10:23 CST
Dear All,
I am trying to use pairInteraction option of NAMD on a trajectory output
from an NVE run and was trying to follow the interaction between a pair of
residues in my protein which is embedded in a membrane.
The configuration file is included at the end of this email for reference.
I am getting huge VDW and TOTAL3 energies for some snapshots and it
doesn't make sense because the log from the original NVE run didn't show
this behavior. Besides, the protein-lipid system has been well
equilibrated for many nanoseconds.
Here is an example output for interaction energies for some snapshots that
shows the range of answers I am getting:
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC KINETIC
TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
ENERGY: 1000 0.0000 0.0000 0.0000 0.0000
0.0060 -0.0000 0.0000 0.0000 0.0000
0.0060 0.0000 0.0060 0.0060 0.0000
ENERGY: 2000 0.0000 0.0000 0.0000 0.0000
-331.7372 99999999.9999 0.0000 0.0000 0.0000
99999999.9999 0.0000 99999999.9999 -99999999.9999 0.0000
ENERGY: 5000 0.0000 0.0000 0.0000 0.0000
29.4931 1.7362 0.0000 0.0000 0.0000
31.2293 0.0000 31.2305 99999999.9999 0.0000
ENERGY: 49000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 99999999.9999 0.0000
ENERGY: 59000 0.0000 0.0000 0.0000 0.0000
-17.7699 53.6117 0.0000 0.0000 0.0000
35.8417 0.0000 36.0596 99999999.9999 0.0000
ENERGY: 62000 0.0000 0.0000 0.0000 0.0000
215.7875 99999999.9999 0.0000 0.0000 0.0000
99999999.9999 0.0000 99999999.9999 -99999999.9999 0.0000
As you can see, sometimes TOTAL3 by itself is large and positive and at
other times when VDW is huge, TOTAL3 becomes a large negative number.
There are no bad VDW contacts in this well equilibrated system.
The configuration file for interaction energy calculation looks like:
#--------------------------------------------------------------------------
# interaction config
coordinates interaction2.pdb
temperature 0
# output params
outputname hccr1_apo_analyze
binaryoutput no
# integrator params
timestep 1.0
# force field params
paratypecharmm on
structure ../Rapo+POPC+wat+Cl.psf
parameters par_all22_prot.inp
parameters par_all27_lipid.inp
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 13.5
stepspercycle 20
# Atoms in group 1 have a 1 in the B column; group 2 has a 2.
pairInteraction on
pairInteractionFile interaction2.pdb
pairInteractionCol B
pairInteractionGroup1 1
pairInteractionGroup2 2
# First frame saved was frame 1000.
set ts 1000
coorfile open dcd eq02_stride100.dcd
# Read all frames until nonzero is returned.
while { ![coorfile read] } {
# Set firstTimestep so our energy output has the correct TS.
firstTimestep $ts
# Compute energies and forces, but don.t try to move the atoms.
run 0
incr ts 1000
}
coorfile close
#---------------------------------------------------------------
Any help is appreciated to resolve the large VDW and large TOTAL3
problems.
Thanks very much,
Ravi
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