[gmx-users] Free Energy of Liquid Water
André Farias de Moura
moura at ufscar.br
Fri Oct 2 15:26:31 CEST 2015
Apart from stability/convergence issues, I guess that turning off all
intermolecular interactions should take you to the ideal gas
straightforwardly, but in a different (P,T) point as compared to your
target. But if you managed to alchemically turn water into an ideal gas,
then you just need to apply standard free change for an ideal gas along a
(P,T) process to achieve your target state.
(I have not found the reference, but I read a paper doing just that with
Monte Carlo simulations a few years ago)
you should be able to track the conversion of water into an ideal gas by
means of the g(r) profiles, which should change from the typical TIP4P
profiles to g(r)=1 for all distances ranging from zero to half of the
smallest box length.
On Thu, Oct 1, 2015 at 11:44 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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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
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