AMBER Archive (2004)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Jan 21 2004 - 07:44:22 CST

It should also be noted that same executable + same random seed + same
architecture WON'T produce the same results on parallel runs (ie., under
mpi). This has to do with order of operations issues in the networking, at
a minimum, and loadbalancing issues, where it is used in programs like
pmemd.
Regards - Bob
----- Original Message -----
From: "Andreas Svrcek-Seiler" <svrci_at_tbi.univie.ac.at>
To: <amber_at_scripps.edu>
Sent: Wednesday, January 21, 2004 5:40 AM
Subject: Re: AMBER: Do I need to repeat MD simulation?

> 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
>
> )))))
> (((((
> ( O O )
> -------oOOO--(_)--OOOo----------------------------------------------------
-
> o Wolfgang Andreas Svrcek-Seiler
> o (godzilla)
> svrci_at_tbi.univie.ac.at
> .oooO Tel.:01-4277-52733
> ( ) Oooo.
> -------\
---( )--------------------------------------------------------
> \_) ) /
> (_/
>
>
>
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