many short runs or one long run?

From: Ching Wong (wongcw_at_TITAN.SFASU.EDU)
Date: Mon Jul 10 2006 - 15:04:42 CDT

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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