[gmx-users] crystal lattice topology generation

Bala subramanian bala.biophysics at gmail.com
Tue Mar 20 17:49:49 CET 2018

Dear Grom. users,


I have to simulate a crystal lattice with gromacs. In the unit cell, there
are 16 copies of the mineral (Lets say 16 residues). If all residues have
the same number of atoms, I can simply create the .rtp file for one residue
and then proceed for the topology generation.

In my lattice, residues at one edge, for instance, interact those in the
other side of the crystal due to periodicity. Hence, I am stuck not knowing
the apt strategy to create the topology. Any insights to deal with this
issue based on your experience could be of much help to me.



C. Balasubramanian

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