[gmx-users] TPI and chemical potential

Gmx QA gmxquestions at gmail.com
Mon Aug 15 13:31:12 CEST 2016

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.
[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….


[1] Chemical potential of liquids and mixtures via Adaptive Resolution ...

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