[gmx-users] Covalent bond/crosslink formation with calcium

Justin Lemkul 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
> afterwards?

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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