From: Chris Harrison (charris5_at_gmail.com)
Date: Tue Mar 16 2010 - 23:58:40 CDT
Daniel,
The script initially minimizes the system (the first phase of movement).
The script then begins MD; however constraints are turned on, presumably
with perhaps too strong a force constant for your system which explains the
second phase lacking movement. During this phase the loop heats the system
from it's minimized value of 0K to 300K in increments of 20K. The idea is
to gradually introduce thermal energy into the system instead of
instantaneously hopping from 0K to 300K. Whether or not the gradual or
instantaneous warming is the correct approach depends upon the specifics of
your system. However, if you are seeing no movement, I would ascribe it to
constraints with too strong a force constant. Following heating of the
system, the constrains are then scaled down to 0 in 4 steps, explaining the
reappearance of movement.
Chris
--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu Voice: 217-244-1733
http://www.ks.uiuc.edu/~char Fax: 217-244-6078
On Tue, Mar 16, 2010 at 7:17 AM, Daniel Hornburg <Hleinad_at_gmx.de> wrote:
> 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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