Hi Justin, I take it that both the sets of parameters should produce identical macroscopic quantities. For the GPU, is this a decent .mdp?
cutoff-scheme = Verlet vdwtype = switch rlist = 1.2 ;rlistlong = 1.4 NOT USED IN GPU...IS THIS OK? rvdw = 1.2 ;rvdw-switch = 1.0 NOT USED IN GPU...IS THIS OK? coulombtype = pme DispCorr = EnerPres rcoulomb = 1.2 On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] < ml-node+s5086n5012351...@n6.nabble.com> wrote: > > > On 11/7/13 11:32 PM, Rajat Desikan wrote: > > > Dear All, > > The setting that I mentioned above are from Klauda et al., for a POPE > > membrane system. They can be found in charmm_npt.mdp in lipidbook (link > > below) > > http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html > > > > Is there any reason not to use their .mdp parameters for a > membrane-protein > > system? Justin's recommendation is highly valued since I am using his > > forcefield. Justin, your comments please > > > > Careful now, it's not "my forcefield." I derived only a very small part > of it :) > > > To summarize: > > Klauda et al., suggest > > rlist = 1.0 > > rlistlong = 1.4 > > rvdw_switch = 0.8 > > vdwtype = Switch > > coulombtype = pme > > DispCorr = EnerPres ;only usefull with reaction-field > > and pme or pppm > > rcoulomb = 1.0 > > rcoulomb_switch = 0.0 > > rvdw = 1.2 > > > > Justin's recommendation (per mail above) > > vdwtype = switch > > rlist = 1.2 > > rlistlong = 1.4 > > rvdw = 1.2 > > rvdw-switch = 1.0 > > rcoulomb = 1.2 > > > > The differences between these two sets of run parameters are very small, > dealing > mostly with Coulomb and neighbor searching cutoffs. I would suspect that > any > difference between simulations run with these two settings would be > similarly > small or nonexistent, given that rcoulomb is a bit flexible when using > PME. The > value of rlist is rarely mentioned in papers, so it is good that the > authors > have provided the actual input file. Previous interpretation of CHARMM > usage > generally advised setting rcoulomb = 1.2 to remain consistent with the > original > switching/shifting functions. That setting becomes a bit less stringent > when > using PME. > > -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 > > [hidden email] <http://user/SendEmail.jtp?type=node&node=5012351&i=0> | > (410) 706-7441 > > ================================================== > -- > gmx-users mailing list [hidden > email]<http://user/SendEmail.jtp?type=node&node=5012351&i=1> > 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 [hidden > email]<http://user/SendEmail.jtp?type=node&node=5012351&i=2>. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012351.html > To unsubscribe from CHARMM .mdp settings for GPU, click > here<http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=5012267&code=cmFqYXRkZXNpa2FuQGdtYWlsLmNvbXw1MDEyMjY3fDM0NzUwNzcwNA==> > . > NAML<http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> > -- 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