[gmx-users] Free Energy of Liquid Water
mrshirts at gmail.com
Tue Oct 6 21:05:41 CEST 2015
For a pure fluid, G = N \mu. And \mu = (dG/dN)_(T,P). So you only
need to change one molecule to ideal gas to get the change in free
energy. The free energy of transfer of water from liquid to gas is
indeed the free energy of solvation of one water molecule in bath of
water. So there's a reason why you're just finding tutorials of
solvation free energies!
On Thu, Oct 1, 2015 at 10:44 PM, Nathan K Houtz <nhoutz at purdue.edu> wrote:
> Hi everyone,
> I would like to use Gromacs to do Thermodynamic Integration (TI) from liquid water (TIP4P model) to an ideal gas, to find the relative free energy. To do this, I believe one generally integrates above the critical point by increasing the temperature above the critical temperature and then relaxing the pressure until the system is a diffuse gas. The mdp options documentation is helpful, and I went through an ethanol solvation tutorial, but there doesn't appear to be a "pressure-lambda" or a "volume-lambda" option that I could use to do the second part. How can I get Gromacs to calculate the dh/dl derivative while relaxing the pressure?
> In addition, all of the tutorials I found for thermodynamic integration were for finding solvation free energies. The coulomb and VDW forces are essentially changed from "completely on" to "completely off". But in my case, I'd like to change the temperature and pressure between two nonzero values. I don't want to begin my simulation at 0K and 0atm, but lambda *must* go from 0 to 1. How can I define both starting and ending points for the temperature and pressure (or volume, or density)?
> Thanks for your help!
> Nathan H.
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