I haven't tried that before. May be you can open the .gro files before and after genbox with a text editor. Then, check those water molecules? Those water molecules might have the same residue id.
On Mon, Aug 17, 2015 at 1:42 PM, Jorge Fernandez de Cossio Diaz < cos...@cim.sld.cu> wrote: > Hi all, > I have a crystallographic PDB file which comes some waters molecules. I > want to run an MD simulation which includes those water molecules. After > generating the topology file (which includes the waters) and defining the > box shape, I fill the box with solvent using genbox. At this point it > becomes impossible to track down visually where the water molecules are. My > question is if the file that genbox outputs still contains the > crystallographic water molecules? Or are they replaced by the molecules > added by genbox? > Thanks in advance. Best, cossio > --------------------------------------------------- > > [http://5.cim.co.cu/cim.gif] > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.