Re: [gmx-users] Significant smaller area per lipid in bilayer simulations using CHARMM force field
On 9/20/16 4:03 PM, 凌未风 wrote: Hi Justin, I am using a temperature of 323 K, but I am using SSM instead of PSM. Does this make difference? No, but there is no reason why PSM should work and SSM wouldn't. PS: not sure this is the best way to reply in a mailing list It works like any other email. Just reply to gmx-us...@gromacs.org (which should be the default reply-to address) and the mailing list sends it out to everyone. -Justin On 9/20/16 1:17 PM, ??? wrote: Hello: I am simulating a stearol sphingomyelin bilayer with 81 lipids in each leaflet using the CHARMM force field. I used the CHARMM-GUI to generate the initial conformation, as well as the parameters for mdp file. I conducted the simulation by gmx5.0.4. I found a significant smaller area per lipid (APL) in my simulations. The APL kept on decreasing, and started to equilibriated after 400 ns. The expected value is ~55.4 A^2, but in my simulation, the value was ~50.8 A^2 after equilibrated. For me this difference is significant. I looked up in the mailing list, and found someone said that it is because of the ions using or it is because of the motion of the two leaflets. So I tried simulations without ions, and with NaCl/KCl. I also tried to remove the centers of mass of two leaflets separately in my simulations. But all of the simulations generated similar APL. I am really appreciate for any possible suggestions. This looks really strange for me, as I am using the "standard parameters" (i.e., the parameters generated by CHARMM-GUI) for CHARMM force filed in gromacs, and the difference should not be so larger, if there are any differences The values should be in better agreement; we validated PSM as part of the latest CHARMM-GUI update. You're using the .mdp files directly from CHARMM-GUI, right? What temperature have you set? -Justin Thanks again for any help you may provide. Cheers, RXG University of Calgary -- == 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.
Re: [gmx-users] Significant smaller area per lipid in bilayer simulations using CHARMM force field
Hi Justin, I am using a temperature of 323 K, but I am using SSM instead of PSM. Does this make difference? Cheers, RXG PS: not sure this is the best way to reply in a mailing list On 9/20/16 1:17 PM, ??? wrote: > Hello: > > > I am simulating a stearol sphingomyelin bilayer with 81 lipids in each > leaflet using the CHARMM force field. I used the CHARMM-GUI to generate the > initial conformation, as well as the parameters for mdp file. I conducted the > simulation by gmx5.0.4. > > > I found a significant smaller area per lipid (APL) in my simulations. The APL > kept on decreasing, and started to equilibriated after 400 ns. The expected > value is ~55.4 A^2, but in my simulation, the value was ~50.8 A^2 after > equilibrated. For me this difference is significant. I looked up in the > mailing list, and found someone said that it is because of the ions using or > it is because of the motion of the two leaflets. So I tried simulations > without ions, and with NaCl/KCl. I also tried to remove the centers of mass > of two leaflets separately in my simulations. But all of the simulations > generated similar APL. > > > I am really appreciate for any possible suggestions. This looks really > strange for me, as I am using the "standard parameters" (i.e., the parameters > generated by CHARMM-GUI) for CHARMM force filed in gromacs, and the > difference should not be so larger, if there are any differences > The values should be in better agreement; we validated PSM as part of the latest CHARMM-GUI update. You're using the .mdp files directly from CHARMM-GUI, right? What temperature have you set? -Justin > > Thanks again for any help you may provide. > > > Cheers, RXG University of Calgary > -- == 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.
Re: [gmx-users] Significant smaller area per lipid in bilayer simulations using CHARMM force field
On 9/20/16 1:17 PM, 凌未风 wrote: Hello: I am simulating a stearol sphingomyelin bilayer with 81 lipids in each leaflet using the CHARMM force field. I used the CHARMM-GUI to generate the initial conformation, as well as the parameters for mdp file. I conducted the simulation by gmx5.0.4. I found a significant smaller area per lipid (APL) in my simulations. The APL kept on decreasing, and started to equilibriated after 400 ns. The expected value is ~55.4 A^2, but in my simulation, the value was ~50.8 A^2 after equilibrated. For me this difference is significant. I looked up in the mailing list, and found someone said that it is because of the ions using or it is because of the motion of the two leaflets. So I tried simulations without ions, and with NaCl/KCl. I also tried to remove the centers of mass of two leaflets separately in my simulations. But all of the simulations generated similar APL. I am really appreciate for any possible suggestions. This looks really strange for me, as I am using the "standard parameters" (i.e., the parameters generated by CHARMM-GUI) for CHARMM force filed in gromacs, and the difference should not be so larger, if there are any differences The values should be in better agreement; we validated PSM as part of the latest CHARMM-GUI update. You're using the .mdp files directly from CHARMM-GUI, right? What temperature have you set? -Justin Thanks again for any help you may provide. Cheers, RXG University of Calgary -- == 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] Significant smaller area per lipid in bilayer simulations using CHARMM force field
Hello: I am simulating a stearol sphingomyelin bilayer with 81 lipids in each leaflet using the CHARMM force field. I used the CHARMM-GUI to generate the initial conformation, as well as the parameters for mdp file. I conducted the simulation by gmx5.0.4. I found a significant smaller area per lipid (APL) in my simulations. The APL kept on decreasing, and started to equilibriated after 400 ns. The expected value is ~55.4 A^2, but in my simulation, the value was ~50.8 A^2 after equilibrated. For me this difference is significant. I looked up in the mailing list, and found someone said that it is because of the ions using or it is because of the motion of the two leaflets. So I tried simulations without ions, and with NaCl/KCl. I also tried to remove the centers of mass of two leaflets separately in my simulations. But all of the simulations generated similar APL. I am really appreciate for any possible suggestions. This looks really strange for me, as I am using the "standard parameters" (i.e., the parameters generated by CHARMM-GUI) for CHARMM force filed in gromacs, and the difference should not be so larger, if there are any differences Thanks again for any help you may provide. Cheers, RXG University of Calgary -- 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.
