[gmx-users] Block averaging

[sun]

Allright. I have made 20 ns blocks for 200 ns trajectory and one 0-200 ns whole trajectory. Now I have average of each block and I can calculate std dev and std error from these results. But I am confused how to represent this data and what is the standard value to conclude something meaningful, I mean it should be visually represented. So, How can I plot it in the form of a graph or visually represnt it? Is there any way or shall I give only the values? I am sorry if my question is very basic but I have searched a lot of papers and I cant understand.

Suniba

Sent from my iPhone

> On 24-Jun-2016, at 4:51 pm, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
>> On 6/24/16 6:23 AM, sun wrote:
>> 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.
> 
> Whatever is physically/biologically meaningful for your system.
> 
> -Justin
> 
>> 
>> 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
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>>> University of Maryland, Baltimore
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>>> Baltimore, MD 21201
>>> 
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
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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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