[gmx-users] Free Energy of Liquid Water
Nathan K Houtz
nhoutz at purdue.edu
Thu Oct 8 05:08:34 CEST 2015
Thanks for explaining, (and Professor Farais de Moura as well) that makes sense.
On a different note, I've noticed a huge difference in performance between my equillibration run and my actual simulation, and I'm wondering if this is normal. For comparison, I ran a couple small (meaningless) simulations where the only difference was the collection of free energy information and Gromacs slows down by a factor of 39. I had been under the impression that I would be able to do each simulation in just under an hour but now it looks like it will take the better part of two days, which is too much. I'll just have to run shorter or fewer simulations if I can't improve that, but I'm hoping I'm just doing something wrong. I'm essentially using modified versions of the .mdp file I found for this tutorial: http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy. I changed things like turning off the pressure coupling, changing the temperature, etc. The settings for free energy calculations are unchanged. Is the calculation of dh/dl really that expensive, or is this abnormal?
Thank you for the help as always. Regards,
----- Original Message -----
From: "Michael Shirts" <mrshirts at gmail.com>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Cc: "gromacs org gmx-users" <gromacs.org_gmx-users at maillist.sys.kth.se>
Sent: Tuesday, October 6, 2015 3:05:38 PM
Subject: Re: [gmx-users] Free Energy of Liquid Water
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.
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users