[gmx-users] Free Energy of Liquid Water

[Nathan K Houtz]

You were right, it's much faster when I only calculate free energy for one molecule. My simulation has 1000 water molecules in it, but I created a new topology file and gave one molecule a different name (but identical properties) and now it runs the same simulation in about 36% more time, which is much more manageable. Thank you very much for the help! I don't think there is a problem with my topology or mdp files now. 

Regards,
Nathan H.

----- Original Message -----
From: "Michael Shirts" <mrshirts at gmail.com>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, October 7, 2015 11:14:29 PM
Subject: Re: [gmx-users] Free Energy of Liquid Water

If ALL the particles are changing with the free energy coupling
parameter, then GROMACS will slow down quite a bit.  If only one
molecule is changing, then it shouldn't be that much slower (20-30%
slower?)  But without .mdp and.top files, it's hard to say exactly
what is happening.


On Wed, Oct 7, 2015 at 11:08 PM, Nathan K Houtz <nhoutz at purdue.edu> wrote:
> 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 
 re
>  ally that expensive, or is this abnormal?
>
> Thank you for the help as always. Regards,
> Nathan H.
>
> ----- 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.
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