[gmx-users] (no subject)
mark.j.abraham at gmail.com
Mon May 14 10:13:26 CEST 2018
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.
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
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