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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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