Not answering your main question here, just pointing out that you should try:
trjconv -pbc mol -ur compact and then visualize with VMD to see if you are actually getting what you want after all. Chris. -- original message -- I already pack the mixed solvent by using packmol cause the box that i used octahedron.Therefore the error that coming out is that topology and the gro file does not same. When I view the solvent by VMD its just shows that the mixture only fill in the cubic form even though the starting box that i need was octahedron. So I would like to ask you guys if I already pack all the molecule,i need to create the new topology right? before start to minimize? Regards, SHika -- 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
