er 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 witho
lations 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"
> To: "Discussion list for GROMACS us
e help as always. Regards,
Nathan H.
- Original Message -
From: "Michael Shirts"
To: "Discussion list for GROMACS users"
Cc: "gromacs org gmx-users"
Sent: Tuesday, October 6, 2015 3:05:38 PM
Subject: Re: [gmx-users] Free Energy of Liquid Water
For a pure fluid, G =
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
erature to different
> temperatures for each run? What does the temperature-lambda affect in that
> case?
>
> Thanks for your help! Regards,
> Nathan H.
>
> - Original Message -
> From: "André Farias de Moura"
> To: "Discussion list for GROMACS
t case?
Thanks for your help! Regards,
Nathan H.
- Original Message -
From: "André Farias de Moura"
To: "Discussion list for GROMACS users"
Sent: Friday, October 2, 2015 9:26:28 AM
Subject: Re: [gmx-users] Free Energy of Liquid Water
Apart from stability/con
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 app
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
