Re: [gmx-users] Set up anti parallel membrane system for CompEL simulation
Hi Jochen, Thank you for the suggestions. Best, Zheng On Mon, May 4, 2020 at 5:24 PM Jochen Hub 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/ > --- > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Set up anti parallel membrane system for CompEL simulation
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/ --- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Set up anti parallel membrane system for CompEL simulation
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 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/ --- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
