From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Dec 06 2005 - 15:28:50 CST
Hi Eric,
>From what temperature are you "cooling" from? Can I ask why you don't
just equilibrate to the desired temperature (some kind of simulated
annealing)?
Just curious if the atom is protein or solvent. If it is solvent is it
near an interface? The cooling may have a possible side effect in that
one atom might get the residue energy (I know that sounds far fetched).
Regards
Brian
On Tue, 6 Dec 2005, Eric Perim wrote:
> Hello,
>
> I posted a message about having problems with my simulation, and
> followed the advice given by Lewyn of doing a longer simulation. I
> just finished doing an 1000000 timestep (1ns) equilibration (constant
> temperature and pressure) of my system, but still I get an error
> message saying the atoms are moving too fast when I try to start
> another simulation, this one to cool the system (using tcouple). The
> end of the log file is as follows:
> ENERGY: 980000 5007.0883 3041.1113 146.1419
> 14.6181 -59797.6788 6167.0269 9451988.1543
> 0.0000 13539.6654 9420106.1274 310.1190
> 9420679.0896 9420679.0896 310.1190 -3082206.2226
> -3081720.6492 142397.7388 -3082206.2226 -3081720.6492
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> ERROR: Atom 6478 velocity is -401.956 -4511.72 16669.9 (limit is 10000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Exiting prematurely.
> ==========================================
> WallClock: 16.802896 CPUTime: 10.117187 Memory: 7665 kB
>
> I'd like to know if anyone know how to solve this, since I can't
> carry on my research without doing these simulations.
> By the way does anyone know where can I get a routine for
> calculating the pair distribution of the system after simulation?
>
> Thanks in advance,
> Eric
>
************************************************
Brian Bennion, Ph.D.
Bioscience Directorate
Lawrence Livermore National Laboratory
P.O. Box 808, L-448 bennion1_at_llnl.gov
7000 East Avenue phone: (925) 422-5722
Livermore, CA 94550 fax: (925) 424-6605
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