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> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.