GROMACS version: 2019.3
GROMACS modification: No
Hi I’m trying to create a mixed crystal but I’m not managing. I have the unit cell of a crystal of a small (highly linear) molecule (each unit cell is made up of 4 identical molecules with each having a different orientation in space), and I want to replace some of the molecules with a similar, slightly smaller molecule. I have the gro file of the second molecule as well, which I obtained from its unit cell file, so the conformation of the second molecule isn’t random, but follows the exact conformation of the other crystal.
What I want to do is remove some molecules from the original crystal box and replace them with molecules of the second molecule, in the exact same space and orientation, i.e. not with a random orientation, or the removal of more molecules from the original crystal to make space for the second molecule. Given that the second molecule is slightly smaller than the original molecule it should fit nicely (even leave a bit of space), but every time I try with insert-molecules I’m not managing to insert it in the position I want or without the removal of other extra molecules from the original crystal.
I’m guessing I need to use the -ip flag but I’m not really sure how to go about it (I’ve tried it already, but with little success).
Any ideas on how to do this please?