[gmx-users] Block averaging

[sun]

Allright Sir
Thank you

Sent from my iPhone

> On 22-Jun-2016, at 7:09 pm, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
>> On 6/22/16 5:02 AM, sun wrote:
>> Hello users and experts I have completed a 200 ns protein ligand simulation
>> using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational
>> change in protein in the presence of ligand and the results are as expected
>> and correlates to previous references as well. So, shall i believe that
>> simulation is converged or there is need to do block averaging over time
>> intervals? If block averaging is required, the parameters like RMSD and
>> propensities for secondary structure are sufficient to conclude that
>> simulation is converged? Or could anyone please tell me a suitable procedure
>> for making blocks and how to average those. With Regards Suniba
> 
> Just because a simulation produces expected results does not mean it is converged.  You must show that any quantities of interest from which you draw your conclusions, are not systematically varying with time.
> 
> -Justin
> 
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> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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