genbox works best when the box size of the solute is defined as the same as of the water one used to solvate it. So you can build a water box with the dimensions you want and them use it.
You can build a water box by using genconf -nbox and use a script to cut to the dimensions you need, minimize, equilibrate ... Using a bigger box size should work too but it might need to be positioned/centered correctly and the solute too ... On Apr 29, 2013, at 11:30, Alexander Björling <alex.bjorl...@gmail.com> wrote: > Dear users, > > I am trying to solvate a MARTINI model, using a pre-equilibrated > coarse-grained water box. This usually works fine with the following > command. > > genbox -cs water-1bar-303K.gro -cp 01min.gro -o 02solv -vdwd 0.21 > > When I recently increased the box size things started going wrong. As the > simulation box got bigger than the (-cs) water box, the solvated structure > ended up containing clear block-shaped regions of higher and lower solvent > density. I obviously tried stacking the (-cs) box first to make it bigger > than the box in the (-cp) file, > > genconf -f water-1bar-303K.gro -o water-1bar-303K_big.gro -nbox 3 3 3 > > but the problem persisted. Waters actually coincide in the solvated > structure, so energy minimization is obviously hopeless. > > Is genbox behaving unexpectedly or is this likely an input problem? > Cheers, > Alex > -- > 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
