Justin Lemkul wrote > I have seen this exact problem posted before. The coordinates of the > water box > provided by MARTINI have some coordinate values that basically coincide > across > the periodic box. With genconf, you can apply the -dist option to space > them > out slightly, then re-equilibrate before using the new configuration as > input > into genbox.
I don't think that's true. Stacking boxes with -nbox 3 3 3 (without -dist) gives a big box which you can minimize and equilibrate with no trouble. Both with and without -dist 0.21 0.21 0.21 (0.21 is a suitable MARTINI -vdwd for genbox), you get big water boxes which behave well. The problems start when you use them as solvents in genbox. Xavier's suggestion (stack, minimize, equilibrate, manually cut with a script) works fine, thanks for the suggestion. Seems to me there might be a bug in genbox, but I'm not the right person to make such claims. Alex -- View this message in context: http://gromacs.5086.x6.nabble.com/genbox-box-size-problem-tp5007753p5007768.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
