Re: error : atom moving too fast

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Thu May 06 2010 - 06:34:45 CDT

On Thursday 06 May 2010 12:32:13 ipsita basu wrote:
> Thanks a lot for your reply. I tried timestep 1 before your reply and
> the job was running fine without giving any error. But the structure
> become distorted, it squeezes along z axis. Now according to your
> reply I am fix the langevin temp to zero and heating the system
> gradually by loop. This part is given below:
> # gradual temp increase
> run 1000
> for { set TEMP 0 } { $TEMP <= 290 } {incr TEMP 1 } {
> langevinTemp $TEMP
> run 1000
> I hope this will not disturb the structure.
> Any suggestion from your end would be appreciated.
>

Mmmmh, you probably should double check your structure.
I never ran into problems setting temperature, langevinTemp and
LangevinPistonTemp to 303 Kelvin from start.

Make sure to minimize your structure long enough.
At one point it could be necessary to tune the minimization parameters (in
case of bad contacts which are not removed during a normal minimization).
Once I was forced to use CHARMM with the SD minimizer to get my structure
minimized correctly (after this I could run the simulation in NAMD).

To preserve the structure of you protein you should apply constraints to the
protein backbone (C-Alphas, ~10 kcal/(mol*Angs^2)) and reduce them step by
step. Something like this:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
constraints on
consref cons.pdb
conskfile cons.pdb
conskcol B
constraintScaling 1.0

# Minimization
minimize 2000
reinitvels $temp

run 20000
constraintScaling 0.5
run 20000
constraintScaling 0.2
run 20000
constraintScaling 0.1
run 20000
constraintScaling 0.05
run 20000
constraintScaling 0 ;#"Removes" the constraints
run 398000
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Full example:
http://dpaste.com/191524/

Plot the values of the output file and check that everything is in an
acceptable state.

Cheers
Bjoern Olausson

-- 
Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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