[gmx-users] TPI and chemical potential

Tue Aug 16 12:35:56 CEST 2016

Yes, all water atoms can't be with coordinates 0,0,0. I don't know how did
that even work... Weird.

1 ns is very short time scale. Also, how many insertions are you trying per
frame? That could also help improve the sampling.

The inf values are normal as it just means that the water is too structured
and it's hard to insert a new water from the sampling point of view.

Can you post the .mdp you used for the tpi?

João

On Tue, Aug 16, 2016 at 9:52 AM, Gmx QA <gmxquestions at gmail.com> wrote:

> 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-7-2gqMPOAhVFWiwKHdp4DYY4FBAWCBww
> AA&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-request at gromacs.org.
>

-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613