[gmx-users] TPI and chemical potential

[Gmx QA]

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
gromacs?



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:
> <snip>
>   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. [1] (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….
>
> Thanks
> /PK
>
>
>
>
>
> [1] Chemical potential of liquids and mixtures via Adaptive Resolution ...
> <https://www.google.se/url?sa=t&rct=j&q=&esrc=s&source=web&cd=21&ved=0ahUKEwj-7-2gqMPOAhVFWiwKHdp4DYY4FBAWCBwwAA&url=https%3A%2F%2Fopus4.kobv.de%2Fopus4-zib%2Ffiles%2F5097%2FZIB-Report_14-25.pdf&usg=AFQjCNECRk9dif8TGxKJeeztHV6T_FmVuw&sig2=-vsjUB9HRdlcnt4vyKWcbw>
>