(no subject)

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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