[gmx-users] Can somebody explain how to set (XY) hexagonal symmetry pbc in gromacs ?
mark.j.abraham at gmail.com
Thu Aug 11 17:58:29 CEST 2016
The trick is to recognise that a hexagonal cell is equivalent to the
triclinic cell that is formed from the centres of four adjacent hexagonal
cells. You need to describe that triclinic cell. Probably the recipes you
can find in the archive are doing just that.
On Fri, 5 Aug 2016 11:41 CROUZY Serge 119222 <serge.crouzy at cea.fr> wrote:
> 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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