[gmx-users] Free Energy of Liquid Water
Nathan K Houtz
nhoutz at purdue.edu
Tue Oct 6 05:01:34 CEST 2015
Thank you, Professor Farais de Moura. That method of integrating to an ideal gas makes sense. However, I'm having trouble figuring out how to deal with the temperature. I hope my question isn't too basic, but I can't find any examples online and I know I am misunderstanding how it works. I want to integrate from about 200K to 1000K or so (above the critical temperature, which I believe is somewhere in the 700's of Kelvin for TIP4P water). To do this, I thought I would set the reference temperature to 1000, and increment temperature-lambda from 0.2 to 1, thinking that temperature-lambda would scale the absolute temperature. But after running a the simulations, it's evident that temperature-lambda does not affect the thermostat. Should I set the reference temperature to different temperatures for each run? What does the temperature-lambda affect in that case?
Thanks for your help! Regards,
----- Original Message -----
From: "André Farias de Moura" <moura at ufscar.br>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Friday, October 2, 2015 9:26:28 AM
Subject: Re: [gmx-users] Free Energy of Liquid Water
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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