[gmx-users] Can somebody explain how to set (XY) hexagonal symmetry pbc in gromacs ?

CROUZY Serge 119222 serge.crouzy at cea.fr
Fri Aug 5 12:40:58 CEST 2016

Hello Gromacs users

Going from Charmm to Gromacs, I'm trying to simulate a membrane protein inserted into a membrane : I already got the gro and topol file for gromacs for my entire system : Prot + lipids + Water - minimization in rectangular pbc also works fine

Now I'm stuck on how to tell Gromacs to respect hexagonal symmetry  (nice way to lower number of water molecules and lipids in my system) ?

membrane is in the XY plane, Z is principal axis of the inserted protein

crystal define in CHARMM as
CRYSTAL DEFINE HEXA  78 78 127  90.0 90.0 120.0
So my unit cell is a hexagone in the XY plane  (39  Angstrom side)

Reading previous exchanges on the forum I guess the first stage could be something like
gmx editconf -f system -o out -bt tric -box 7.8 7.8 12.7 -angles 90 90 120
(I don't know why triclinic would do the trick)
But what next ?

Any help greatly appreciated

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