GROMACS version: 2021.3
GROMACS modification: No
Hi everyone!
I’m trying to run an MD simulation of perylene (C12H20) starting from it’s crystal structure, which I have defined in a .cif file. To complicate things further, I’m using OPLS where I have the parametrization defined in a .gro and a .itp file for a single perylene molecule.
Is there a way in which I can tell Gromacs to insert individual perylene molecules (defined by my .gro/.itp files) according to the crystal structure defined in the .cif file?
The only option I have found so far is to use gmx insert-molecules, but from what I can tell I can only control molecule position and not rotation (which seems to either be random or no rotation at all).
Cheers!