[gmx-users] (no subject)

Srijan Singh srijancristi at gmail.com
Mon May 14 09:49:32 CEST 2018

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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