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
