Re: [gmx-users] Lennard-Jones potential for protons

2013-07-03 Thread Dr. Vitaly Chaban
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

Re: [gmx-users] Lennard-Jones potential for protons

2013-07-03 Thread Mark Abraham
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 wrote: > Dear Gromacs Users, > > > > Hi, I'm

[gmx-users] Lennard-Jones potential for protons

2013-07-03 Thread Jong Wha Lee
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 par