[gmx-users] crystal lattice topology generation

Alex nedomacho at gmail.com
Tue Mar 20 18:47:55 CET 2018

Prior to generating the topology (say, with x2top) use editconf on your 
coordinates to put the crystal in a box of size that's compatible with 
the periodicity and the number of unit cells in your crystal sample.


On 3/20/2018 10:49 AM, Bala subramanian wrote:
> Dear Grom. users,
> Greetings,
> 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.
> Thanks,
> Bala

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