[gmx-users] energy minimization problem
Justin Lemkul
jalemkul at vt.edu
Sat Nov 2 20:50:55 CET 2013
On 11/2/13 3:38 PM, kiana moghaddam wrote:
> Hi GMX Users
>
> I 'm running MD Simulation for DNA-ligand interaction. I ran energy minimization with emtol=10, 100 and 250 in 10000 steps (steepest descent followed by the conjugate gradient algorithm). The lowest value for energy obtained for emtol=10.
> I have some questions about energy minimization step. what is suitable value for emtol in em.mdp file? how many steps is needed for energy minimization? and how do I understand the minimization is successful?
>
The purpose of EM is to generate a reasonable configuration that can be
subjected to dynamics. For most standard MD, an emtol in the neighborhood of
100-1000 is sufficient, and there are no hard and fast rules that I know of that
motivates that choice. If MD fails, run EM again with a lower tolerance. For
more sensitive calculations like free energy simulations and normal modes, you
will want to minimize much more thoroughly (for NM, emtol < 1) and in double
precision.
As long as the potential energy is negative and in a range that is expected
given the size of the system (10^5 - 10^6 in the case of most solvated proteins
or membranes), the outcome is probably acceptable.
The number of steps is largely irrelevant; the energetic outcome is far more
important. I usually set nsteps to some huge value and just let EM converge as
far as it will.
-Justin
--
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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