[gmx-users] Covalent bond/crosslink formation with calcium
jalemkul at vt.edu
Fri Feb 6 22:33:49 CET 2015
On 2/6/15 10:44 AM, Turgay Cakmak wrote:
> Thank you for the swift reply!
> We have decided against defining covalent bonds and went with the
> calcium-within-peptide-fiber configuration, but we have run into another
> problem, in that some of the calcium cations vanish from the unit cell that
> the fiber is in, and appear in the next unit cell, when we run an energy
> minimization. The missing cations are all on the same side of the peptide
> fiber and form a neat half-cylinder on the adjecent unit cell, so we are
> fairly certain that the problem has to do with our box definition.
> However, the entire structure is within our dodecahedral box prior to
> energy optimization. Is there any reason that the calciums would change
> position after energy minimization? Do we have to redefine our box
Without seeing the actual commands used to set this up and post-process with
trjconv, and probably some images of "before" and "after," it's hard to be
specific. Sounds like a normal consequence of periodicity and possibly
incorrect unwrapping via trjconv.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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