[gmx-users] Block averaging

[sun]

Sir
If I do averaging of no. of clusters in case of protein (increased no. of clusters as compared to pro-lig complex) at regular intervals of time, It will be sufficient to assess if my simulation is converged? In my case clustering in addition to secondary structure are conclusive parameters. 


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
> 
> -- 
> ==================================================
> 
> 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
> 
> ==================================================
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.