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 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 On Fri, Nov 8, 2013 at 2:20 AM, Gianluca Interlandi [via GROMACS] < ml-node+s5086n5012329...@n6.nabble.com> wrote: > Hi Mark! > > I think that this is the paper that you are referring to: > > dx.doi.org/10.1021/ct900549r > > Also for your reference, these are the settings that Justin recommended > using with CHARMM in gromacs: > > vdwtype = switch > rlist = 1.2 > rlistlong = 1.4 > rvdw = 1.2 > rvdw-switch = 1.0 > rcoulomb = 1.2 > > As you mention the switch function in gromacs is different than in CHARMM > but it appears that the difference is very small. > > Gianluca > > On Thu, 7 Nov 2013, Mark Abraham wrote: > > > Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM > > switch differs from the GROMACS switch (Justin linked a paper here with > the > > CHARMM switch description a month or so back, but I don't have that link > to > > hand). > > > > Mark > > > > > > On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan <[hidden > > email]<http://user/SendEmail.jtp?type=node&node=5012329&i=0>>wrote: > > > > >> Thank you, Mark. I think that running it on CPUs is a safer choice at > >> present. > >> > >> > >> On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham <[hidden > >> email]<http://user/SendEmail.jtp?type=node&node=5012329&i=1> > >>> wrote: > >> > >>> Hi, > >>> > >>> It's not easy to be explicit. CHARMM wasn't parameterized with PME, so > >> the > >>> original paper's coulomb settings can be taken with a grain of salt > for > >> use > >>> with PME - others' success in practice should be a guideline here. The > >> good > >>> news is that the default GROMACS PME settings are pretty good for at > >> least > >>> some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and > the > >> GPU > >>> auto-tuning of parameters in 4.6 is designed to preserve the right > sorts > >> of > >>> things. > >>> > >>> LJ is harder because it would make good sense to preserve the way > CHARMM > >>> did it, but IIRC you can't use something equivalent to the CHARMM LJ > >> shift > >>> with the Verlet kernels, either natively or with a table. We hope to > fix > >>> that in 5.0, but code is not written yet. I would probably use vdwtype > = > >>> cut-off, vdw-modifier = potential-shift-verlet and > >> rcoulomb=rlist=rvdw=1.2, > >>> but I don't run CHARMM simulations for a living ;-) > >>> > >>> Mark > >>> > >>> > >>> On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan <[hidden > >>> email]<http://user/SendEmail.jtp?type=node&node=5012329&i=2> > >>>> wrote: > >>> > >>>> Dear All, > >>>> > >>>> Any suggestions? > >>>> > >>>> Thank you. > >>>> > >>>> -- > >>>> View this message in context: > >>>> > >>> > >> > http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html > >>>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > >>>> -- > >>>> gmx-users mailing list [hidden > >>>> email]<http://user/SendEmail.jtp?type=node&node=5012329&i=3> > >>>> 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=5012329&i=4>. > > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>> -- > >>> gmx-users mailing list [hidden > >>> email]<http://user/SendEmail.jtp?type=node&node=5012329&i=5> > >>> 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=5012329&i=6>. > > >>> * Can't post? Read 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 [hidden > >> email]<http://user/SendEmail.jtp?type=node&node=5012329&i=7> > >> 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=5012329&i=8>. > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > -- > > gmx-users mailing list [hidden > > email]<http://user/SendEmail.jtp?type=node&node=5012329&i=9> > > 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=5012329&i=10>. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > ----------------------------------------------------- > Gianluca Interlandi, PhD [hidden > email]<http://user/SendEmail.jtp?type=node&node=5012329&i=11> > +1 (206) 685 4435 > http://artemide.bioeng.washington.edu/ > > Research Scientist at the Department of Bioengineering > at the University of Washington, Seattle WA U.S.A. > ----------------------------------------------------- > -- > gmx-users mailing list [hidden > email]<http://user/SendEmail.jtp?type=node&node=5012329&i=12> > 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=5012329&i=13>. > > * 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-tp5012267p5012329.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 -- View this message in context: http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012335.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
