[gmx-developers] How to put two molecules inside the simulation box with a control on their DISTANCE and ANGLE

Armin Solemanifar armin.solemanifar at gmail.com
Tue Feb 13 00:42:02 CET 2018

Dear Gromacs users,

I'm trying to put two peptides inside the simulation box and have the
ability to rotate them to face each other in a particular way before
starting the simulation. I only know how to put them randomly in the
simulation box.

My second question is how to put them in a certain distance from each other
in the beginning as well.

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