[gmx-users] EM replicates

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Apr 9 07:21:26 CEST 2016

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,

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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