AMBER Archive (2004)

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

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Wed Jan 21 2004 - 04:40:17 CST

Hi,
>
> 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%
regards
Andreas
             
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