[gmx-users] (no subject)

[Srijan Singh]

Thank you,
it worked.

On Mon, May 14, 2018 at 3:43 PM, Mark Abraham <mark.j.abraham at 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 <srijancristi at 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
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