Sorry for the typo below. DFT based *or* semi empirical code. ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Ran Friedman Sent: 02 December 2010 15:01 To: Discussion list for GROMACS users Subject: RE: [gmx-users] proton proton transfer
Hi Olga, It's not straightforward in CHARMM as well. One method is to use conjugate peak refinement, but this will only get you the potential energy surface, but there's also a force field made by Meuwly for dealing with proton transfer IIRC. Depending on the system size, you may want to use QM/MM (implemented in Gromacs) or simulate your system with a DFT-based 'on semi-empricial code. Ran ------------------------------------------------ Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en ------------------------------------------------ ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Olga Ivchenko [olga.ivche...@gmail.com] Sent: 02 December 2010 14:59 To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] proton proton transfer Thnaks, Justin. Probably CHARMM is suitable for this. 2010/12/2 Justin A. Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> Olga Ivchenko wrote: Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrella sampling, but may be there is other techniques? You can't do this with standard MD. Bonds cannot break and re-form in a classical force field. You might be able to do accomplish it with QM, however, but in that case you need to be looking outside of Gromacs. -Justin Yours sincerely, Olga -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org<mailto: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<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 -- 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
