[gmx-users] Set up anti parallel membrane system for CompEL simulation

[Zheng Ruan]

Hi Jochen,

Thank you for the suggestions.

Best,
Zheng

On Mon, May 4, 2020 at 5:24 PM Jochen Hub <jochen.hub at uni-saarland.de>
wrote:

>
>
> Am 04.05.20 um 23:21 schrieb Jochen Hub:
> >
> >
> > Am 04.05.20 um 21:33 schrieb Zheng Ruan:
> >> Hi,
> >>
> >> I'm trying to setup an antiparallel membrane system for CompEL
> >> simulation.
> >> It is relatively straightforward to convert an existing single membrane
> >> system to a parallel system by using
> >>
> >> # gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro
> >>
> >> However, is there an easy way to invert one of the membrane protein
> >> configurations along with the membrane, water and ions?
> >
> > You could try:
> >
> > gmx editconf -rotate 90 0 0
>
> Sorry, I meant of course editconf -rotate 180 0 0
>
> You probably have to combine this with an editconf -translate, together
> with a manual extension of the box by 1-2 Angstroem to avoid overlapping
> water molecules at the box edge.
>
> Jochen
>
> >
> > Cheers, Jochen
> >
> >>
> >> Thanks,
> >> Zheng
> >>
> >
>
> --
> ---------------------------------------------------
> Prof. Dr. Jochen Hub
> Theoretical Biophysics Group
> Department of Physics, Saarland University
> Campus E2 6, Zi. 4.11, 66123 Saarbruecken, Germany
> Phone: +49 (0)681 302-2740
> https://biophys.uni-saarland.de/
> ---------------------------------------------------
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