[gmx-users] crystal lattice topology generation

[Alex]

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.

Alex

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
>
>