[gmx-users] All-bonds vs. H-bonds using CHARMM36
Hi, In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds are constrained for the lipid simulations using SHAKE (excerpt from the paper below) Consistent for all of these simulations was the use of a 1 fs time step and constraining of the hydrogen atoms using the SHAKE algorithm. For a membrane-protein system, is constraining all-bonds via LINCS the right option while using CHARMM36? There was a mention somewhere (I forgot) that constraining all-bonds probably prevents alkane isomerisations in membranes, which could lower the melting temperature. I intend to simulate a POPC bilayer. Can someone with experience please shed some light on this? P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on lipidbook. Their .mdp constrains h-bonds http://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] All-bonds vs. H-bonds using CHARMM36
On 10/31/13 2:21 PM, rajat desikan wrote: Hi, In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds are constrained for the lipid simulations using SHAKE (excerpt from the paper below) Consistent for all of these simulations was the use of a 1 fs time step and constraining of the hydrogen atoms using the SHAKE algorithm. For a membrane-protein system, is constraining all-bonds via LINCS the right option while using CHARMM36? Normally, as the paper states, only bonds involving H are constrained with CHARMM. LINCS is a suitable replacement for SHAKE, though you can use SHAKE in Gromacs if you want. LINCS is generally more robust. There was a mention somewhere (I forgot) that constraining all-bonds probably prevents alkane isomerisations in membranes, which could lower the melting temperature. I intend to simulate a POPC bilayer. Can someone with experience please shed some light on this? Can't comment on this, but I doubt there is any issue if you don't constrain all bonds. P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on lipidbook. Their .mdp constrains h-bonds http://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp It is very uncommon that such input files exist without specifically requesting them; if this is exactly what the authors used, I see no reason to deviate from it unless you have a demonstrably superior protocol. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] All-bonds vs. H-bonds using CHARMM36
Thank you, Justin! I did intend to use h-bonds for the CHARMM36 simulations and all-bonds elsewhere (depending on the FF). I just wanted some clarity before I proceeded. On Fri, Nov 1, 2013 at 1:49 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 2:21 PM, rajat desikan wrote: Hi, In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds are constrained for the lipid simulations using SHAKE (excerpt from the paper below) Consistent for all of these simulations was the use of a 1 fs time step and constraining of the hydrogen atoms using the SHAKE algorithm. For a membrane-protein system, is constraining all-bonds via LINCS the right option while using CHARMM36? Normally, as the paper states, only bonds involving H are constrained with CHARMM. LINCS is a suitable replacement for SHAKE, though you can use SHAKE in Gromacs if you want. LINCS is generally more robust. There was a mention somewhere (I forgot) that constraining all-bonds probably prevents alkane isomerisations in membranes, which could lower the melting temperature. I intend to simulate a POPC bilayer. Can someone with experience please shed some light on this? Can't comment on this, but I doubt there is any issue if you don't constrain all bonds. P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on lipidbook. Their .mdp constrains h-bonds http://lipidbook.bioch.ox.ac.**uk/uploads/package/CHARMM36/** 48-POPE-wurl/v1/charmm_npt.mdphttp://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp It is very uncommon that such input files exist without specifically requesting them; if this is exactly what the authors used, I see no reason to deviate from it unless you have a demonstrably superior protocol. -Justin -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
