[gmx-users] solvating hexagonal biphasic system

Peter Kroon p.c.kroon at rug.nl
Fri Aug 5 12:51:52 CEST 2016

Hi Neha,

If I recall correctly, you can represent any periodic system as cubic -
and this is what Gromacs uses internally.


On 05/08/16 05:42, Neha Gandhi wrote:
> Dear list,
> I am trying to build a system with HAP and a protein. I was able to insert
> protein 10nM above the hexagonal surface. However, when I try to solvate
> the system it puts in cubic box which appears shifted. I am following
> Justin's tutorial on preparing biphasic systems. How can I can solvate
> hexagonal system? Is there something which I am missing out?
> Thanks,
> Neha

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