[gmx-users] free energy calculations for reference state for constant pH MD simulations...

[Ozbil, Mehmet]

Hello,

I am trying to run constant pH MD with GROMACS, and started with the TI free energy calculations. I am following Justin Lemkul`s free energy calculation tutorial, and assuming that the free energy calculations will be similar to calculate the protonation energy of titratable amino acids such as GLU or HIS.

My question is that, while scanning the lambda values for the free energy calculations do I need to define both protonated and deprotonated states of GLU in the same .top and .pdb file, or I just use one .top and one .pdb file and by changing the lambda values from 0.0 to 1.0 it does the deprotonation itself. If I need to incorporate the two states in one .top and .pdb file can anyone help with how to do that?

Thanks,
Mehmet Ozbil