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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