[gmx-users] EM replicates

Gregory Poon gpoon at gsu.edu
Sat Apr 9 14:48:23 CEST 2016

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 

Thanks again!


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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