Thank you, it worked. On Mon, May 14, 2018 at 3:43 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote:
> Hi, > > I don't know whether solvate supports such boxes, but if it does I would > use editconf first to describe the box, and then solvate to fill it. > Currently you are filling a cubic box and then transforming it to another > shape, and that isn't a well formed operation. > > Mark > > On Mon, May 14, 2018 at 7:49 AM Srijan Singh <srijancri...@gmail.com> > wrote: > > > Hello all, > > > > I modeled a hexagonal box of water using the following steps: > > > > gmx solvate -cs spc216.gro -o waterst1 -box 6 6 6 > > > > gmx editconf -f waterst1.gro -o w120.gro -bt tric -box 4.5 4.5 5.56 > -angles > > 90 90 120 -c > > > > After which i used trjconv with -pbc atom -ur compact and obtained the > > hexagonal cylinder. > > > > But while minimizing the system , i encountered large forces (due to > > overlapping atoms ) and on deleting(the overlapped molecule) and > > minimizing the same thing happened again. > > > > when i ran equlibriation instead of minimization (after deleting > overlapped > > molecule), it too crashed. > > > > I'm using tip3p water with opls forcefield. > > I am attaching the topology files and mdp file file for minimization > below. > > I am relatively new to gromacs so if anyone could please point out any > > error which i'm making. > > > > Thanks in advance > > Srijan > > -- > > 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.
