Thank you, Justin, for the prompt answer!
Justin Lemkul wrote > In almost all cases, a dodecahedral box is the optimal choice. A cubic > box with the same periodic distance for an elongated protein would be much > larger. OK, got it. Justin Lemkul wrote > In the absence of the actual editconf commands, it's hard to judge the > utility of each of these setups. > The box vectors shown are the ones that will be used unless you manipulate > them in some way. In this particular case the commands were: g_editconf -f protein.gro -o protein_box.gro -bt triclinic -d 1.0 -c and g_editconf -f protein.gro -o protein_box.gro -bt dodecahedron -d 1.0 -c and my concern is that the reported box volume in case of dodecahedron is much bigger than that for a triclinic one (for the same protein). Sure, the triclinic box volume is calculated from vectors 100% correctly, and I guess that it is correct for dodecahedron as well > And I have one more short question: > Is it possible somehow to visualize the "actual" dodecahedral box at this > stage (i.e. right after adding water, having no trajectory file yet)? > Justin Lemkul wrote > You need a .tpr file and can re-wrap the periodic image with trjconv -pbc > mol -ur compact. So I need to run at least genion first. Got it. Thank you. -- View this message in context: http://gromacs.5086.n6.nabble.com/Actual-box-size-tp5003850p5003856.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
