[gmx-users] Re: CHARMM .mdp settings for GPU
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= 1.0NOT 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=nodenode=5012351i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012351i=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=nodenode=5012351i=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 herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012267code=cmFqYXRkZXNpa2FuQGdtYWlsLmNvbXw1MDEyMjY3fDM0NzUwNzcwNA== . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=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 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] Re: CHARMM .mdp settings for GPU
On 11/9/13 4:16 PM, rajat desikan wrote: 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= 1.0NOT USED IN GPU...IS THIS OK? coulombtype = pme DispCorr = EnerPres rcoulomb= 1.2 I have no basis for saying whether or not it will produce correct results. I have never tested this force field on GPU with the Verlet scheme. My biggest concern is with the treatment of van der Waals interactions, and I have not used the Verlet scheme enough to understand what it is doing and how it will treat the interactions that should be switched. If someone else can comment, that would be useful to me, as well! Test carefully and please report back. A comparison between CPU and GPU would be very valuable. -Justin 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=nodenode=5012351i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012351i=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=nodenode=5012351i=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 herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012267code=cmFqYXRkZXNpa2FuQGdtYWlsLmNvbXw1MDEyMjY3fDM0NzUwNzcwNA== . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- == 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
[gmx-users] Re: CHARMM .mdp settings for GPU
On Sat, 9 Nov 2013, Gianluca Interlandi wrote: Just to chime in. Here is a that paper might be helpful in understanding the role of cuoffs in the CHARMM force field: AU STEINBACH, PJ BROOKS, BR AF STEINBACH, PJ BROOKS, BR TI NEW SPHERICAL-CUTOFF METHODS FOR LONG-RANGE FORCES IN MACROMOLECULAR SIMULATION SO JOURNAL OF COMPUTATIONAL CHEMISTRY SN 0192-8651 PD JUL PY 1994 VL 15 IS 7 BP 667 EP 683 DI 10.1002/jcc.540150702 UT WOS:A1994NU1741 Gianluca On Sat, 9 Nov 2013, Justin Lemkul wrote: On 11/9/13 4:16 PM, rajat desikan wrote: 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= 1.0NOT USED IN GPU...IS THIS OK? coulombtype = pme DispCorr = EnerPres rcoulomb= 1.2 I have no basis for saying whether or not it will produce correct results. I have never tested this force field on GPU with the Verlet scheme. My biggest concern is with the treatment of van der Waals interactions, and I have not used the Verlet scheme enough to understand what it is doing and how it will treat the interactions that should be switched. If someone else can comment, that would be useful to me, as well! Test carefully and please report back. A comparison between CPU and GPU would be very valuable. -Justin 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=nodenode=5012351i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012351i=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=nodenode=5012351i=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 herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012267code=cmFqYXRkZXNpa2FuQGdtYWlsLmNvbXw1MDEyMjY3fDM0NzUwNzcwNA== .
Re: [gmx-users] Re: CHARMM .mdp settings for GPU
On 11/9/13 9:51 PM, Gianluca Interlandi wrote: On Sat, 9 Nov 2013, Gianluca Interlandi wrote: Just to chime in. Here is a that paper might be helpful in understanding the role of cuoffs in the CHARMM force field: AU STEINBACH, PJ BROOKS, BR AF STEINBACH, PJ BROOKS, BR TI NEW SPHERICAL-CUTOFF METHODS FOR LONG-RANGE FORCES IN MACROMOLECULAR SIMULATION SO JOURNAL OF COMPUTATIONAL CHEMISTRY SN 0192-8651 PD JUL PY 1994 VL 15 IS 7 BP 667 EP 683 DI 10.1002/jcc.540150702 UT WOS:A1994NU1741 Yes, that's the one I posted several weeks back. It describes the original implementation of cutoff schemes in CHARMM. -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] Re: CHARMM .mdp settings for GPU
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 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
[gmx-users] Re: CHARMM .mdp settings for GPU
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 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] Re: CHARMM .mdp settings for GPU
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 rajatdesi...@gmail.comwrote: 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 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 -- 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] Re: CHARMM .mdp settings for GPU
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 mark.j.abra...@gmail.comwrote: 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 rajatdesi...@gmail.com 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 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 -- 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 -- 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] Re: CHARMM .mdp settings for GPU
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 rajatdesi...@gmail.comwrote: 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 mark.j.abra...@gmail.com 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 rajatdesi...@gmail.com 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 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 -- 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 -- 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 -- 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] Re: CHARMM .mdp settings for GPU
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 rajatdesi...@gmail.comwrote: 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 mark.j.abra...@gmail.com 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 rajatdesi...@gmail.com 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 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 -- 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 -- 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 -- 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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +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 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
[gmx-users] Re: CHARMM .mdp settings for GPU
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=nodenode=5012329i=0wrote: 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=nodenode=5012329i=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=nodenode=5012329i=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=nodenode=5012329i=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=nodenode=5012329i=4. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012329i=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=nodenode=5012329i=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=nodenode=5012329i=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=nodenode=5012329i=8. * Can't
