[gmx-users] g_potential help
Hi All, I have a membrane-protein-solvent system, and I want the potential across the membrane in the direction of the membrane normal. I have 2 questions in that regard. 1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water interface and ~2 for the hydrophobic membrane core. g_potential returns the result for epsilon_r = 1. How can I incorporate this into the result? 2) Default ng =1? Is the number of groups referring to the number of charge groups defined in the topology? Thank you for your time. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] g_potential help
On 4/21/14, 9:58 AM, rajat desikan wrote: Hi All, I have a membrane-protein-solvent system, and I want the potential across the membrane in the direction of the membrane normal. I have 2 questions in that regard. 1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water interface and ~2 for the hydrophobic membrane core. g_potential returns the result for epsilon_r = 1. How can I incorporate this into the result? I'd venture a guess that the value of epsilon_r in the output is the same as the interpretation of epsilon_r in the .mdp file - it is the relative dielectric permittivity. A value of 1 means don't scale anything; see previous discussions. 2) Default ng =1? Is the number of groups referring to the number of charge groups defined in the topology? No, that means the number of groups you want to analyze, just like g_rdf and other tools sometimes give the option of doing multiple analyses at the same time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] g_potential help
Hi Justin, So different parts of my system in Z-direction should be scaled differently, right? On a coarse level, aqueous part with a scaling of 80, membrane with a scaling of 2? How do I correct for this? Can I take the quantitative output for potential difference across a membrane in water from g_potential literally? Thanks, On Monday, April 21, 2014, Justin Lemkul jalem...@vt.edu wrote: On 4/21/14, 9:58 AM, rajat desikan wrote: Hi All, I have a membrane-protein-solvent system, and I want the potential across the membrane in the direction of the membrane normal. I have 2 questions in that regard. 1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water interface and ~2 for the hydrophobic membrane core. g_potential returns the result for epsilon_r = 1. How can I incorporate this into the result? I'd venture a guess that the value of epsilon_r in the output is the same as the interpretation of epsilon_r in the .mdp file - it is the relative dielectric permittivity. A value of 1 means don't scale anything; see previous discussions. 2) Default ng =1? Is the number of groups referring to the number of charge groups defined in the topology? No, that means the number of groups you want to analyze, just like g_rdf and other tools sometimes give the option of doing multiple analyses at the same time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] g_potential help
On 4/21/14, 5:11 PM, rajat desikan wrote: Hi Justin, So different parts of my system in Z-direction should be scaled differently, right? On a coarse level, aqueous part with a scaling of 80, membrane with a scaling of 2? How do I correct for this? Can I take the quantitative output for potential difference across a membrane in water from g_potential literally? You don't need to scale anything. The force field parameters for every biomolecular force field that I know of are based on epsilon_r = 1, i.e. no special alteration of vacuum permittivity. The results, at face value, should be sufficient. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
