[gmx-users] energy minimization problem

[Justin Lemkul]

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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