Hi, The default behaviour is to consider atom positions, but you want to include atoms based on e.g. molecule position. IIRC use -selrpos mol_cog for that (or similar changes within the selection). See the final examples at http://manual.gromacs.org/documentation/2018/onlinehelp/selections.html#selection-examples
Mark On Thu, Sep 27, 2018 at 8:28 PM Alex <alexanderwie...@gmail.com> wrote: > Thanks Mark. > The gmx select and then gmx trjconv work fine and I have a box with a more > or less desirable region being solvated by water. > However there is only one problem and that is the SOL's molecules in the > border of the region ( resname SOL and z>= 2 ). By that the Water molecules > in the border are split; for instance a OW and one HW1 are in one side of > the border (to be considered in the gmx select) and the HW2 is in another > side of the border (to not be considered in the gmx select). Do you know > how I can either consider or discard those whole SOL's OW,HW1 and HW2 all > together? > > Thanks. > Alex > > > On Thu, Sep 27, 2018 at 12:20 PM Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > No, but you can use gmx select to make such a selection from the > > fully-solvated box, and gmx editconf (maybe) or gmx trjconv (definitely) > to > > end up with the content you want. (We'd like to make this functionality > > more generally available, but it's not ready yet...) > > > > Mark > > > > On Thu, Sep 27, 2018 at 6:10 PM Alex <alexanderwie...@gmail.com> wrote: > > > > > Dear all, > > > I wonder if it is possible to solvate just a part of a box using gmx > > > solvate. For example suppose you have a box with the lengths of x, y, > z, > > > then, how I can solvate only a part of it like (x, y, z with z> 2)? > > > > > > Thanks > > > Alex > > > -- > > > 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. > > > -- > 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.