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 -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
