Re: AMBER: Do I need to repeat MD simulation?

From: Andreas Svrcek-Seiler <>
Date: Wed, 21 Jan 2004 11:40:17 +0100 (CET)

> A general question.Do I need to repeat my simulation several times to
> prove the changes of protein I observed significant, not some artifical
> things?
....Definitely, if the change is "irreversible".
If the changes are "reversible", like repeated folding and unfolding
(that would be a cool observation)
or repeated conversions between well defined distinct conformations,
you might simply continue the existing trajectory for a much longer time.
Generally, don't accept the outcome of MD simulations as proof for
anything (or be *very* cautious at least).

> And will two trajectory files be identical if I run twice with
> identical input files?
....Same executable + same random seed + same architecture: yes.
Executable compiled with different compiler options (or another
compiler): trajectories might slowly diverge from each other.
Different random seeds (i.e. identical coordinates but not completely
identical input files): No.
However, relevant results must be independent of the random seed.

....just my 0.02%
           ( O O )
              o Wolfgang Andreas Svrcek-Seiler
              o (godzilla)
      .oooO Tel.:01-4277-52733
      ( ) Oooo.
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Received on Wed Jan 21 2004 - 10:53:01 PST
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