[gmx-users] No equilibration, annealing

Justin Lemkul jalemkul at vt.edu
Thu Mar 13 18:33:09 CET 2014

On 3/13/14, 1:26 PM, ehs wrote:
> Hi gmx users,
> Is it possible to jump directly from energy minimization to product
> simulation? Would solution be different with or without temperature
> annealing?

Anything is possible, but not everything is wise.  The purpose of equilibration 
is to relax the solvent (which is in an artificial lattice state when produced 
by genbox) around the solute.  Energy minimization does not (and cannot) do a 
complete job of optimizing the solvent.  Without equilibration with restraints 
on the solute, you risk encountering artificial forces that will send your 
dynamics down a non-physical path, or (more likely) the simulation will just crash.

If you simply generate velocities and kick off the simulation after EM, I would 
strongly suspect the outcome would be different than if you had properly 
equilibrated or annealed the system.  For most simple systems, I find no real 
reason to use annealing, but some systems benefit from it.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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