Re: [gmx-users] Ion conduction through a protein-membrane system
Thanks Peter for your explanation. Sincerely, Shima - Original Message - From: Peter C. Lai To: Discussion list for GROMACS users Cc: Sent: Tuesday, October 2, 2012 10:10 AM Subject: Re: [gmx-users] Ion conduction through a protein-membrane system On 2012-10-01 11:16:43PM -0700, Shima Arasteh wrote: > > > Dear users, > > I want to study ion conduction through a protein-memrane system. > First of all, I tried to simulate a usual protein-membrane system. I'd like > to know if it is possible to add asymmetrical number of ions to leaflets of > membrane? Yes. You need to first use trjorder -z to reorder the waters, then you need to make 2 index group of consecutive atoms in each layer. Tell genion to only pick waters from the separate index groups. It is important that the index groups representing the water surrounding the "top" and "bottom" leaflet are consecutive in atom number or else genion will refuse to run. The easiest way to do that is to find Z around the middle of the bilayer where there are no waters and separate the top waters from the bottom waters. Note that use of pbc=xyz Periodic Boundary Conditions will allow the "extracellular" ions to travel into the "intracellular" space as the top ions diffuse +Z (and the "intracellular" ions can diffuse -Z into the "extracellular" space), so track your ion movements appropriately. Finally if the total charge of the system isn't balanced, grompp will throw a notice or a warning. I don't know what the consequences of running a simulation of a non-neutral system has on things like energy conservation... > Secondly, is it possible to apply an external electrical field to study ion > conduction in a system? > The manual appears suggests such a thing might be possible to some extent. You'll probably want to look for yourself to see if your use-case is supported. -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Ion conduction through a protein-membrane system
Thanks Casten. Sincerely, Shima - Original Message - From: Carsten Kutzner To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Tuesday, October 2, 2012 11:02 AM Subject: Re: [gmx-users] Ion conduction through a protein-membrane system Hi Shima, there is also a patch for Gromacs available to study ion conduction through membrane channels that you might find useful. Please take a look at this page: http://www.mpibpc.mpg.de/grubmueller/compel Best, Carsten On Oct 2, 2012, at 8:16 AM, Shima Arasteh wrote: > > > Dear users, > > I want to study ion conduction through a protein-memrane system. > First of all, I tried to simulate a usual protein-membrane system. I'd like > to know if it is possible to add asymmetrical number of ions to leaflets of > membrane? > Secondly, is it possible to apply an external electrical field to study ion > conduction in a system? > > Thanks in advance. > > > Sincerely, > Shima > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Ion conduction through a protein-membrane system
Hi Shima, there is also a patch for Gromacs available to study ion conduction through membrane channels that you might find useful. Please take a look at this page: http://www.mpibpc.mpg.de/grubmueller/compel Best, Carsten On Oct 2, 2012, at 8:16 AM, Shima Arasteh wrote: > > > Dear users, > > I want to study ion conduction through a protein-memrane system. > First of all, I tried to simulate a usual protein-membrane system. I'd like > to know if it is possible to add asymmetrical number of ions to leaflets of > membrane? > Secondly, is it possible to apply an external electrical field to study ion > conduction in a system? > > Thanks in advance. > > > Sincerely, > Shima > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Ion conduction through a protein-membrane system
On 2012-10-01 11:16:43PM -0700, Shima Arasteh wrote: > > > Dear users, > > I want to study ion conduction through a protein-memrane system. > First of all, I tried to simulate a usual protein-membrane system. I'd like > to know if it is possible to add asymmetrical number of ions to leaflets of > membrane? Yes. You need to first use trjorder -z to reorder the waters, then you need to make 2 index group of consecutive atoms in each layer. Tell genion to only pick waters from the separate index groups. It is important that the index groups representing the water surrounding the "top" and "bottom" leaflet are consecutive in atom number or else genion will refuse to run. The easiest way to do that is to find Z around the middle of the bilayer where there are no waters and separate the top waters from the bottom waters. Note that use of pbc=xyz Periodic Boundary Conditions will allow the "extracellular" ions to travel into the "intracellular" space as the top ions diffuse +Z (and the "intracellular" ions can diffuse -Z into the "extracellular" space), so track your ion movements appropriately. Finally if the total charge of the system isn't balanced, grompp will throw a notice or a warning. I don't know what the consequences of running a simulation of a non-neutral system has on things like energy conservation... > Secondly, is it possible to apply an external electrical field to study ion > conduction in a system? > The manual appears suggests such a thing might be possible to some extent. You'll probably want to look for yourself to see if your use-case is supported. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
