[gmx-users] TPI and chemical potential
Gmx QA
gmxquestions at gmail.com
Tue Aug 16 12:45:39 CEST 2016
Hi Joao
Thank you for your reply. My mdp-file is pasted below:
integrator = tpi
emtol = 1000.0
emstep = 0.01
nsteps = 50000
nstlist = 1
cutoff-scheme = group
ns_type = grid
coulombtype = pme
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
nstxtcout = 5000
; Temperature coupling is on
tcoupl = V-rescale
tc-grps = system
tau_t = 0.1
ref_t = 298
; Pressure coupling is on
pcoupl = no
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
ld_seed = -1
I am using the amber99sb forcefield for tip3p, so I believe the 1.0 nm
cutoffs to be correct?
I have tried a couple different values for the number of insertions, and
for some frames different values sometimes give non-inf results, but for
the most part it does not seem to make a difference.
1 ns is short, I agree, but since the value of <mu> (which I take to be the
excess chemical potential I am after) immediately goes to inf when the
first mu=inf appears, extending does not make sense to me? Is the chemical
potential reported elsewhere as well?
Thanks
/PK
2016-08-16 12:35 GMT+02:00 João M. Damas <jmdamas at itqb.unl.pt>:
> 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>
> > >
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>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
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