Re: [gmx-users] Number of ions in Anionic lipid system- Charmm-GUI
On 7/5/17 12:17 PM, Nidhin Thomas wrote: Hi Justin, Thanks a lot for the prompt reply. I used just 400 POPC lipids to build the lipid bilayer and when I added 150 mM KCl, it added 49 K+ and 49 Cl- to the system. Do you think these numbers are correct? Could you please tell me how I can check the correct number of ions? Look at the CHARMM-GUI output, note how it calculates volume, and pull out a calculator for moles/volume :) Neutral lipids require no counterions, so everything you add is just the desired salt concentration. The size of the original system (300 POPC + 100 POPG) was (11.7480468 11.7480468 8.98 ) nm. If the size of the system is very small to accommodate the ions, how can I change the size of the system in charmm-gui ? Or should I just get the bilayer system and add ions by myself using gonion command in gromacs? IIRC you can control how many hydrating waters you get per lipid. If you increase the number of waters, this will increase the volume. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
[gmx-users] Number of ions in Anionic lipid system- Charmm-GUI
Hi Justin, Thanks a lot for the prompt reply. I used just 400 POPC lipids to build the lipid bilayer and when I added 150 mM KCl, it added 49 K+ and 49 Cl- to the system. Do you think these numbers are correct? Could you please tell me how I can check the correct number of ions? The size of the original system (300 POPC + 100 POPG) was (11.7480468 11.7480468 8.98 ) nm. If the size of the system is very small to accommodate the ions, how can I change the size of the system in charmm-gui ? Or should I just get the bilayer system and add ions by myself using gonion command in gromacs? Thanks, Nidhin Thomas >> Dear GROMACS Users, >> >> I have created a lipid bilayer system (300 POPC + 100 POPG) using CHARMM-GUI. >> I want to include 0.150 M KCl in the system. When I use the option in >> charmm-gui, it gives 98K+ ions and -2 Cl ion. But when I calculated the >> number of ions using the size of simulation box, I am getting 98 ions. >> >> Can anyone tell me what I should do to get the exact number of ions in the >> system? >> > > CHARMM-GUI calculates an excluded volume due to the solute (protein, nucleic > acid, lipids, etc) so using the total box volume is incorrect when > calculating > the number of ions in solution. The result you're getting tells you that > your > box is too small (insufficient solvent volume) to achieve 150 mM KCl. > >> Would it be correct if I first neutralize the system using 100 K+ ions and >> then add 0.15 M KCl ions (49 K+ and 49 Cl-) in the system? >> > > No, because then your effective concentration is much higher than what you > want. > > -Justin -- 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] Number of ions in Anionic lipid system- Charmm-GUI
On 7/4/17 9:20 PM, Nidhin Thomas wrote: Dear GROMACS Users, I have created a lipid bilayer system (300 POPC + 100 POPG) using CHARMM-GUI. I want to include 0.150 M KCl in the system. When I use the option in charmm-gui, it gives 98K+ ions and -2 Cl ion. But when I calculated the number of ions using the size of simulation box, I am getting 98 ions. Can anyone tell me what I should do to get the exact number of ions in the system? CHARMM-GUI calculates an excluded volume due to the solute (protein, nucleic acid, lipids, etc) so using the total box volume is incorrect when calculating the number of ions in solution. The result you're getting tells you that your box is too small (insufficient solvent volume) to achieve 150 mM KCl. Would it be correct if I first neutralize the system using 100 K+ ions and then add 0.15 M KCl ions (49 K+ and 49 Cl-) in the system? No, because then your effective concentration is much higher than what you want. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
[gmx-users] Number of ions in Anionic lipid system- Charmm-GUI
Dear GROMACS Users, I have created a lipid bilayer system (300 POPC + 100 POPG) using CHARMM-GUI. I want to include 0.150 M KCl in the system. When I use the option in charmm-gui, it gives 98K+ ions and -2 Cl ion. But when I calculated the number of ions using the size of simulation box, I am getting 98 ions. Can anyone tell me what I should do to get the exact number of ions in the system? Would it be correct if I first neutralize the system using 100 K+ ions and then add 0.15 M KCl ions (49 K+ and 49 Cl-) in the system? Thanks a lot!.. Nidhin Thomas -- 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.
