[gmx-users] TPI and chemical potential
gmxquestions at gmail.com
Tue Aug 16 09:52:28 CEST 2016
Please - anyone?
I gathered from the mail-list that maybe the entire molecule (water in this
case) should be centered on origo (rather than having all atoms at (0,0,0),
but this gives me only a lot of inf for the chemical potential.
How can I calculate the excess chemical potential of water using TPI in
2016-08-15 13:31 GMT+02:00 Gmx QA <gmxquestions at gmail.com>:
> Dear list
> I am trying to teach myself how the test particle method for excess
> chemical potential calculations work. To this end, I created a small system
> of about 900 water molecules (TIP3p), and simulated for 1 ns.
> I then set up files for inserting an extra water molecule to calculate mu,
> the chemical potential.
> The end of my tpi_start.gro looks like this:
> 884SOL OW 2650 2.466 0.788 2.747 -0.5599 -0.0387 0.0570
> 884SOL HW1 2651 2.529 0.835 2.802 0.0024 -0.9901 0.2261
> 884SOL HW2 2652 2.506 0.703 2.732 -1.4472 -0.3598 -0.5022
> 885SOL OW 2653 0.000 0.000 0.000 0.0000 0.0000 0.0000
> 885SOL HW1 2654 0.000 0.000 0.000 0.0000 0.0000 0.0000
> 885SOL HW2 2655 0.000 0.000 0.000 0.0000 0.0000 0.0000
> 3.01188 3.01188 3.01188
> So I think this last water molecule is the one to be inserted. The
> topology was also updated accordingly.
> I then made a rerun like this:
> $ gmx mdrun -v -deffnm tpi -rerun md.xtc
> And the output is a series of lines like this:
> Reading frame 180 time 900.000 mu 8.924e+00 <mu> 7.240e+00
> mu 7.671e+00 <mu> 7.242e+00
> mu 6.987e+00 <mu> 7.241e+00
> mu 7.010e+00 <mu> 7.239e+00
> mu 7.691e+00 <mu> 7.241e+00
> mu 7.439e+00 <mu> 7.242e+00
> mu 6.757e+00 <mu> 7.240e+00
> mu 8.114e+00 <mu> 7.243e+00
> mu 7.173e+00 <mu> 7.243e+00
> mu 8.768e+00 <mu> 7.249e+00
> Reading frame 190 time 950.000 mu 7.799e+00 <mu> 7.252e+00
> mu 9.284e+00 <mu> 7.259e+00
> mu 8.103e+00 <mu> 7.262e+00
> mu 7.835e+00 <mu> 7.265e+00
> mu 7.321e+00 <mu> 7.265e+00
> mu 7.576e+00 <mu> 7.267e+00
> mu 9.348e+00 <mu> 7.274e+00
> mu 7.021e+00 <mu> 7.272e+00
> mu 7.162e+00 <mu> 7.272e+00
> mu 7.695e+00 <mu> 7.274e+00
> Reading frame 200 time 1000.000 mu 7.104e+00 <mu> 7.273e+00
> Now, is <mu> here the average computed chemical potential? What is the TPI
> energy distribution being reported in the tpi.xvg-file?
> I tried to google for the chemical potential of water and according to
> e.g.  (page 13) it should be around -23.5 kJ/mol. I would really
> appreciate if someone could comment on this, as I need to understand it
> before moving on to more relevant (for me) systems….
>  Chemical potential of liquids and mixtures via Adaptive Resolution ...
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