Re: [gmx-users] Re: Charmm 36 forcefield with verlet cut-off scheme
On 9/20/13 7:59 AM, Mark Abraham wrote: Note that the group scheme does not reproduce the (AFAIK unpublished) CHARMM switching scheme, either. In case anyone is interested, the reference cited in the CHARMM papers for the switching and shifting functions is dx.doi.org/10.1002/jcc.540150702. -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 36 forcefield with verlet cut-off scheme
With what was said: what do you all think of the following parameters for Charmm 36: rlist = 1.2 rlistlong = 1.4 vdwtype = cutoff rvdw-switch = 1.0 rvdw = 1.2 rcouloumb = 1.2 vdw-modifier = Potential-shift-Verlet DispCorr = No cutoff-scheme = Verlet -- View this message in context: http://gromacs.5086.x6.nabble.com/Charmm-36-forcefield-with-verlet-cut-off-scheme-tp5011322p5011413.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 36 forcefield with verlet cut-off scheme
On 9/23/13 4:04 PM, akk5r wrote: With what was said: what do you all think of the following parameters for Charmm 36: rlist = 1.2 rlistlong = 1.4 vdwtype = cutoff rvdw-switch = 1.0 rvdw = 1.2 rcouloumb = 1.2 vdw-modifier = Potential-shift-Verlet DispCorr = No cutoff-scheme = Verlet rvdw-switch has no effect here, and I have no real hard evidence to know whether or not this will produce the same effect as the traditional settings. You would have to carefully demonstrate that what you're doing doesn't break the force field. -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 36 forcefield with verlet cut-off scheme
Note that the group scheme does not reproduce the (AFAIK unpublished) CHARMM switching scheme, either. Mark On Fri, Sep 20, 2013 at 4:26 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/19/13 9:55 PM, akk5r wrote: Thanks Justin. I was told that the vdwtype = switch was an essential component of running Charmm36. Is that not the case? It is, but I suppose one can achieve a similar effect with the Verlet scheme. You can certainly use the traditional CHARMM settings if you use the group scheme, instead. The vdw-modifier setting should give you a comparable result, but I have never tried it myself. -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 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 36 forcefield with verlet cut-off scheme
Thanks Justin. I was told that the vdwtype = switch was an essential component of running Charmm36. Is that not the case? -- View this message in context: http://gromacs.5086.x6.nabble.com/Charmm-36-forcefield-with-verlet-cut-off-scheme-tp5011322p5011328.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 36 forcefield with verlet cut-off scheme
On 9/19/13 9:55 PM, akk5r wrote: Thanks Justin. I was told that the vdwtype = switch was an essential component of running Charmm36. Is that not the case? It is, but I suppose one can achieve a similar effect with the Verlet scheme. You can certainly use the traditional CHARMM settings if you use the group scheme, instead. The vdw-modifier setting should give you a comparable result, but I have never tried it myself. -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
