[gmx-users] Re: Minimum simulation time needed to have a completely minimized structure

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 10 16:32:14 CET 2010

bharat gupta wrote:
> so how shall i proceed now ... can u guide ??

No.  If you have a specific question, then ask it, but this forum shouldn't be 
viewed as a tool to teach you everything about how to run simulations.  I would 
suggest that you consult any of the numerous textbooks about simulation 
methodology, the Gromacs manual, the list archive where there are tons of 
threads about successes and failures in EM, and finally the literature.  Many 
papers will describe the criteria used to finish EM, be it the number of steps, 
method used, target Fmax, etc.

If your EM isn't working for some reason, or you encounter a specific problem, 
please post a detailed description of what the problem is and what you've tried 
to do to fix it.  If you want free help, you have to demonstrate that you're 
willing to exhaust your resources first and make it easy to help you.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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