[gmx-users] How many ps needs a simulation?

[Tsjerk Wassenaar]

Hi Jahan,

You mention your computer restarted. Now that sounds serious. Can you give
more details about that? What happens in the log-file before the crash. Was
it gromacs or something else that caused it? Are you running windows or
*nix?

Furthermore, as mentioned before, how long the simulation should be, depends
on what you want to get from it. If you try to fold your sequence, I'd guess
you need at least 5-10 seconds.., and a few lifetimes of simulation if we
don't get much faster computers soon. Still, if you're interested in
functional processes, you're facing very long relaxation times, which I
estimate could well be about 20-25 ns or more (as I've seen for a quite
globular protein of my own, about half the size of yours). That means that
before you get some real information you need simulation times of 40-50 ns
at least. You can check the relaxation or convergence of your simulation by
looking at the cosine content of the principal components (g_anaeig -h). If
you're interested in local phenomena, you may be able to get away with
shorter time scales.

By the way, if your protein is more or less rigid, you can cut down the
computational cost by choosing a proper definition of your simulation box.
If your interested you can contact me off the list for that (but keep other
questions regarded to the simulations directed to the list please).

Tsjerk

On 5/11/06, Dallas B. Warren <Dallas.Warren at vcp.monash.edu.au> wrote:
>
> Mark,
>
> > rofl... didn't see until now we both had the same response to
> > this question!
>
> Yeah, spun me out a bit too when your repsonse arrived after I had sent
> mine ;-)
>
> Catch ya,
>
> Dr. Dallas Warren
> Lecturer
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9524
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.
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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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