We have noticed that g_genbox issue with MARTINI but have not new able to understand where it actually comes from. It might be a bug or just a miss communication of the vdw radius with genbox that appears only with large spheres.
On Apr 29, 2013, at 19:50, "alex.bjorling" <alex.bjorl...@gmail.com> wrote: > 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 -- 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
