AW: [gmx-users] Shape of box
frausch at ipb-halle.de
Wed Apr 4 12:40:53 CEST 2012
Please see "editconf -h" for the available box shapes. Which of these you use is depending on your system (or a matter of taste actually).
The dodecahedron is mostly used to decrease the system volume, thus it's a good choice for the simulation of a single protein in solvent (as in your tutorial?).
Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Im Auftrag von Lara Bunte
Gesendet: Mittwoch, 4. April 2012 11:24
An: gmx-users at gromacs.org
Betreff: [gmx-users] Shape of box
If you add solvent water around your protein you have to generate a box with the editconf command. How to know what shape that box should have? In my tutorial is a dodecahedron used. What other boxes exist and how to know which box one has to use?
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