[gmx-users] Energy minimization

Justin Lemkul jalemkul at vt.edu
Fri Feb 22 19:50:52 CET 2013

On 2/21/13 9:10 PM, Kieu Thu Nguyen wrote:
> Dear all,
> I can not distinguish when the Fmax < 10 kJmol-1nm-1,  < 100,  < 1000 ? is
> appropriate
> Can anyone tell me which value is appropriate for lipid membrane, for
> protein in water, for protein in lipid membrane ?

There is no absolute rule.  The purpose of EM is just to get the simulation 
system into a configuration that is sufficiently relaxed such that dynamics 
don't implode.  For sensitive free energy calculations and normal mode analysis, 
you need the Fmax to be as low as possible.  For most protein systems, Fmax < 
1000 is generally reasonable for normal MD, but that's just an empirical 



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


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