Re: [gmx-users] MD simulation with varying pH

On 07/05/2012 05:03 PM, J Peterson wrote: Dear GROMACS Users, I'm planning to work on a protein that activates itself under lower pH conditions. And I don't have any clues how to do it in GROMACS. My first question is about the possibilities to do this in GROMACS, has anyone done this before? It

Re: [gmx-users] MD simulation with varying pH

Dear Peterson, There's no magic wand for this. You'll need to find out pKa values of titrable amino acids in your protein (in literature, MEAD software, etc.). Then, you can protonate (pHpKa) those group according to the pH. -G On Thu, Jul 5, 2012 at 12:33 PM, J Peterson wrote: > Dear GROMACS

[gmx-users] MD simulation with varying pH

Dear GROMACS Users, I'm planning to work on a protein that activates itself under lower pH conditions. And I don't have any clues how to do it in GROMACS. My first question is about the possibilities to do this in GROMACS, has anyone done this before? It can even be a constant simulations at a par