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 <gmxquesti...@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> > -- 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.