[gmx-users] MD - analysis

[Justin A. Lemkul]

Kavyashree M wrote:
> Dear Sir,
> 
>    g_mindist analysis showed the violation of minimum image convention, it
> was violated over a short period of time and then it came back to normal.
> I attach the plot herewith. Should this data be discarded or any useful 
> information
> can be obtained.
> 

You've got a considerable number of data points wherein the periodic image 
distance is less than the longest cutoff, so I don't think you can simply shrug 
this off.  The data were influenced by spurious interactions.  Watch the 
trajectory, see what's happening during this period, and accommodate for such 
events in a new simulation based on what you learn.

-Justin

> Thank you
> With Regards
> M. Kavyashree
> 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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