[gmx-users] Multiple MD simulation
jalemkul at vt.edu
Mon Apr 29 14:20:48 CEST 2019
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
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
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