From: Daniel Hornburg (Hleinad_at_gmx.de)
Date: Tue Mar 16 2010 - 07:17:02 CDT
Sorry I think there was a problem with my mail account resulting in not
sending the parts of the mail were I added my script. Hope this time it
worked!
"Hello,
I am using NAMD for md and I am relatively new. I have a question concerning
my equilibrium script. When I am watching the resulting trajectory in VMD
(there is no error or something like that produced, all seems to be fine)
after a short movement (probably the minimization see #1) the motion of the
whole system stops for a while. Then it continues with movements at the
point where constrains are decreased (probably, #2).
I think, that the whole loop with the reassignTemp $TEMP is not working
instead the whole system stays at 0.0 kelvin for this loop. I got that
script from another person who is more skilled than me but not available
right now. Anyway I am asking myself what the benefit of this whole loop was
intended to be and I hesitate to change something right on my own without
feedback.
Hope you might help me. Have great day and Thank you!
Best wishes,
Daniel"
constraints on
consref crd/mwt26ra.pdb
conskfile crd/mwt26ra.pdb
conskcol O
constraintScaling 5
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 14.0
rigidBonds all
fullElectFrequency 1
nonbondedFreq 1
langevin on
langevinTemp 0
langevinDamping 5
cellBasisVector1 104.0 0.0 0.0
cellBasisVector2 0.0 60.0 0.0
cellBasisVector3 0.0 0.0 60.0
PME on
PMEGridSpacing 1.0
timestep 1.00
temperature 0.0
#1 minimation which I can see in vmd/trjfile
minimize 100000
#2 loop wich might not work
for { set TEMP 30 } { $TEMP < 300 } { incr TEMP 20 } {
reassignTemp $TEMP
run 10000
}
#here I think the movment starts again
langevinTemp 295
run 200000
constraintScaling 4
run 200000
constraintScaling 3
run 200000
constraintScaling 2
run 200000
constraintScaling 1
run 200000
constraintScaling 0
run 200000
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