[gmx-users] EnMin & constraints: Hamletic doubt

Justin Lemkul jalemkul at vt.edu
Thu Jun 19 15:06:36 CEST 2014

On 6/19/14, 4:11 AM, Nicola Staffolani wrote:
> Dear GMX community,
> ​I am running simulations of a solvated protein on a (frozen) Au substrate,
> but I think that my question is so basic that it falls outside the details
> of my case...
> So, the question is: when I prepare the system by minimizing the energy,
> should I set constraints = all_bonds, h_bonds or none?

What was your force field parametrized to use?  Most commonly, modern force 
fields constrain bonds involving H, though all bonds are frequently constrained 
in practice because the differences are generally small and the rigid 
representation of a bond is considered by many to be a more realistic 
representation of the ground state than a harmonic function.

> IMHP, I should set it to all_bonds, otherwise I may risk that the system's
> energy minimum corresponds to a configuration very different from the
> initial one... However, I saw  somebody is using constraints = none and I
> was wandering why...

Without context, answering that is impossible.

> Would somebody take the pleasure to embark on the discussion of such an
> issue with me? Thnx in advance,

There have been numerous discussions on the underlying theory of constraints and 
their proper application; a bit of searching should turn them up.  Several have 
occurred very recently on this very list.



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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