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 [email protected] http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en ------------------------------------------------ ________________________________________ From: [email protected] [[email protected]] On Behalf Of Olga Ivchenko [[email protected]] Sent: 02 December 2010 14:59 To: [email protected]; 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 <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[email protected]> 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 [email protected]<mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
