[gmx-users] Re: Minimized structure

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 8 13:05:28 CET 2010

bharat gupta wrote:
> Hi all,
> I had followed all the 7 steps of gromacs beginners tutorial and I
> have a doubt that during the minimization step .. which structure is
> minimized one ?? The one that i used for the minimization step ...

A structure is only minimized if you ran EM, or the program you used to generate 
the structure performed an EM prior to any process in Gromacs.  The output from 
mdrun will be energy-minimized (provided the process completes satisfactorily), 
but as for whether there was any EM done prior to that, Gromacs didn't do it, so 
only you know based on how you generated your structure.


> Pls reply


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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