[gmx-users] EM replicates

[Mark Abraham]

Hi,

These tools are not intended to be deterministic. gmx genion -h etc. will
talk about random components, and how to seed them. Parallel mdrun is not
generally reproducible. But there is nothing useful to conclude from
several EM runs converging to the same structure.

Mark

On Sat, Apr 9, 2016 at 2:48 PM Gregory Poon <gpoon at gsu.edu> wrote:

> Hi Tsjerk,
>
> Thank you for your response.  I notice that between replicates, the
> number of water solvate reports is sometimes not exactly the same
> (though not by much, for the same box size and geometry), and the Fmax
> at which em gives up is also different (up to 50%), at a different
> atom.  Does the water assignment also follow a repeatable randomization
> procedure?
>
> Thanks again!
>
> Gregory
>
>
> On 4/9/2016 1:21 AM, Tsjerk Wassenaar wrote:
> > Hi Gregory,
> >
> > Yes, these steps are deterministic. Think of where the randomization
> should
> > come from. Sure, there is 'random' placement of ions in genion, but it
> has
> > a default seed, resulting in deterministic random numbers :)
> >
> > Hope it helps,
> >
> > Tsjerk
> > On Apr 9, 2016 00:33, "Gregory Poon" <gpoon at gsu.edu> wrote:
> >
> >> Hello all!
> >>
> >> I am wondering if the solvate, genion, and energy minimization (using
> >> steepest descent) procedures are deterministic.  I have been performing
> >> replicate energy minimization of a duplex DNA structure, always starting
> >> from scratch (i.e., pdb2gmx) and using the same parameters in terms of
> >> force field, water choice, ion concentration/type etc. and getting
> >> convergent structures that are super-imposable.  My question is whether
> >> this is something that I would expect in any event, for any system (up
> to
> >> energy minimization, before dynamics simulation), or that I just happen
> to
> >> have a well-behaved system.
> >>
> >> Thanks in advance,
> >> Gregory
> >> --
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> --
>
> *Gregory M. K. Poon, PhD, RPh*
> Associate Professor
> Departments of Chemistry and Nutrition | Georgia State University
> NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
> P.O. Box 3965 | Atlanta, GA 30303
> Ph (404) 413-5491 | gpoon at gsu.edu <mailto:gpoon at gsu.edu>
>
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