[gmx-users] Multiple MD simulation

[Justin Lemkul]

On 4/23/19 2:55 AM, ISHRAT JAHAN wrote:
> Dear all,
> I have done the long 200ns MD simulation of protein in water. I have
> received a comment from the reviewer that for the convergence of the
> results I have to perform multiple simulations using different initial
> conformations. Can anyone tell me the criteria for taking the different
> initial conformations of protein and how to check the convergence of the
> results? Any help regarding this will be highly appreciated.

What defines a different conformation depends on the system being 
investigated. Perhaps that means starting with a different loop 
conformation (if relevant) or some different state of a multi-domain 
protein (open vs. closed) or a different conformer of an IDP. That's up 
to you to determine. It is more common to start with the same 
conformation but different velocities. No single trajectory is 
necessarily believable; replicates are generally expected for any modern 
MD simulation study.

Convergence across the ensemble simply means that the results of 
different simulations do not differ from one another as determined by 
statistical testing.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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