I am also not aware of the force field parameters for hydrated/solvated proton, but maybe I am just wrong here.
An attempt to describe proton with Newtonian dynamics will unlikely give you anything similar to reality. Lennard-Jones parameters play no role here, by the way, some force fields assign zero sigma and zero epsilon to hydrogen, for instance, in water molecule. If you construct a particle, such as H3O+ or H5O2+, etc, it might work somehow. But you definitely need to run some QM calculations on these particles beforehand. Dr. Vitaly V. Chaban On Wed, Jul 3, 2013 at 10:00 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > One does not have a free proton in a condensed phase simulation, which > is what all those force fields target. And even if you do, a > classical-mechanics description of it will probably be poor at best. > > Mark > > On Wed, Jul 3, 2013 at 9:35 AM, Jong Wha Lee <jongwh...@postech.ac.kr> > wrote: > > Dear Gromacs Users, > > > > > > > > Hi, I'm trying to simulate a system with a free proton included. > However, I > > wasn't able to find Lennard-Jones parameters for free protons in charmm, > > amber, and opls ff. On the other hand, there are parameters for other > > cations such as Na, K, etc. > > > > Is there any reason why parameters for free protons are not included? Or > is > > there any way I may find appropriate parameters? > > > > > > > > Thank you very much in advance, > > > > > > > > Jong Wha > > > > -- > > 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 > -- 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
