From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Jul 10 2006 - 15:29:02 CDT
There are some insightful papers/reviews by Valerie Daggett that could
give you a better hint on how to solve your "problem". You can look
for "daggett v" at www.pubmed.com, IŽm sure youŽll find useful papers.
Some of the papers that might help you are the following:
Day R, Daggett V. Proc Natl Acad Sci U S A. 2005;102:13445-50 and
Daggett V. Curr Opin Struct Biol. 2000;10:160-4.
I hope it helps.
2006/7/10, Ching Wong <wongcw_at_titan.sfasu.edu>:
> Hi, all.
> From your experience, do you think it is better to run many shorter run
> or just one longer run (such as four 2ns runs vs. one 8ns run)?
> And do you get the exact same result (trajectory, RMSD, RMSF, etc) from
> a repeated run (same seed)? Is the MD repeatable at all in NAMD?
> I thought I saw it somewhere in the manual that results may differ.
> Can someone confirm that, I just want to make sure. :)
> If the result is not reproducible, what would you say? How can we claim
> the MD simulation experiment is still reliable???? Any ideas please?
> Sincerely yours,
> Quote from Manual
> seed random number seed
> Acceptable Values: positive integer
> Default Value: pseudo-random value based on current UNIX clock time
> Description: Number used to seed the random number generator if
> temperature or langevin is selected. This can be used so that
> consecutive simulations produce the same results. If no value is
> specified, NAMD will choose a pseudo-random value based on the current
> UNIX clock time. The random number seed will be output during the
> simulation startup so that its value is known and can be reused for
> subsequent simulations. Note that if Langevin dynamics are used in a
> parallel simulation (i.e., a simulation using more than one processor)
> even using the same seed will not guarantee reproducible results.
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