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 <[EMAIL PROTECTED]> 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
[EMAIL PROTECTED]
+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
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