[gmx-users] Analysing multiple cavities in ion Channel through CompEl simulations

[Carlos Navarro]

Dear gmx-users,
I'm currently investigating ion permeability in a channel that displays
multiple cavities through ComEl simulations. Unfortunately one can just
define a single cylinder per membrane. Considering the size of my system
(>440k atoms) I don't think is a viable idea to run n independent
simulations for the n cavities want to study, so I guess my only choice is
to run a single simulation creating a big cylinder that comprises all the
cavities, and then by scripting check from which cavity the different ions
are passing. What do you think about this approach? I'm open to suggestions.
Best regards.
Carlos

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Carlos Navarro Retamal

Bioinformatic Engineering. PhD

Postdoctoral Researcher in Center for Bioinformatics and Molecular
Simulations

Universidad de Talca

Av. Lircay S/N, Talca, Chile

T: (+56) 712201 <//T:%20(+56)%20712201> 798

E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl