[Chimera-users] Inifinite lattice minimisation
meng at cgl.ucsf.edu
Thu Aug 2 12:29:50 PDT 2012
It only uses the atoms that are present (does not assume period boundary conditions). I would not recommend using Chimera minimization on a very large system -- it does not use any distance cutoff and is thus quite slow. Also the usual limitations of minimization: it will only go to a nearby local minimum, not the global minimum, so trapping in rather unfavorable conformations is a distinct possibility.
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Aug 2, 2012, at 12:23 PM, Kyle Morris wrote:
> Dear all,
> I am trying to do minimisations on a crystal system. I wonder if when chimera knows the unit cell will it minimise as an infinite lattice or do the copies need to be explicitly created before minimisation proceeds?
> Really appreciate any help/insight.
> Best wishes,
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