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.mdp<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 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://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 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