Tsjerk Wassenaar wrote:
Hi Justin,
Note that the pseudo-sphere representation is for visualization
purposes only; the triclinic cell should be the input for any simulation.
This not true. It doesn't matter which representation you use as
input. Molecules may be broken over PBC, but the topological
information is taken from the .tpr file anyway. Gromacs may spit out
broken molecules, and will swallow them just as well.
Good to know, and that certainly makes sense. I guess I was thinking of an old
post that warned never to do this; perhaps there was some problem with PBC
handling in an older version, and thus I made a habit to never change the input
coordinates.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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