[gmx-users] diffusion coefficient of oxygen

Berk Hess gmx3 at hotmail.com
Wed Mar 10 14:11:56 CET 2010


I would think this is one of very few examples where most of the force field is quite
uncritical. Diffusion of a hydrophobic solute in water will mainly depend on the size
of the solute and the diffusion coefficient of the water model itself.
Of the common water models, SPC/E has the best diffusion coefficient and it
combines well with the Gromos force fields, so use that.

It is well known that the diffusion of SPC is twice what it should be.


> Date: Wed, 10 Mar 2010 07:35:41 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] diffusion coefficient of oxygen
> Sunil Thapa wrote:
> > Respected Experts
> > 
> > I need your help
> > 
> > In my study of diffusion of a oxygen molecule in 255 molecules of water, 
> > I previously used SPC water model with ffgmx force field with cutoff L-J 
> > and Coulomb interaction. I wanted to reproduce the experimental value 
> > 2.4 unit for diffusion coefficient of oxygen in water at 298 K and 1 atm.
> > 
> > To equilibrate the system to the experimental water density of 997 I 
> > used Berendsen thermostat and the same barostat. The density of the 
> > system was 980(+-) 10 kg/m3 which is not the experimental value. After 
> > equilibration, I subjected the system to NVT ensemble md of 100 ns. I 
> > got the msd for oxygen molecule and analyzing first 4 ns (which was a st 
> > line part) of the plot, I got the diffusion coefficient of about 2.45 
> > unit which is close to the experimental value. The question is how can 
> > the diffusion coefficient be so close when density is not produced. Is 
> > this a mere coincidence?
> > 
> More likely a consequence of the water model itself.  Keep in mind that SPC 
> water is not real water, it does not reproduce all properties of water 
> accurately.  No water model does.  Look into the literature for the expected 
> density of SPC, but 980 does sound close to what is expected.
> > Thinking that I used TIP4P water model with the same number but 
> > different force field ffG3a
> > . I equilibrated the system to the same pressure and temperature with 
> > the same algorithms. After equilibration, the correspondng density was 
> > 991(+-) 15 kg/m3. Then I subjected it to the production run of 100ns. 
> > Now what I see is that the MSD curve is a hill, initially increasing, 
> > reaching maximum and again returning to the base. The diffusion 
> > coefficient is 0.7 unit for 100 ns of trajectory.
> > 
> > What would have happened? Is this due to the increased density? Your 
> > precious knowledge on the subject matter would give me a sigh of relief.
> > 
> You must be careful interpreting your results.  If you only have one molecule of 
> your solute, then statistics will likely be very poor.  You probably need either 
> more solute molecules within a given system or many replicates of the same 
> single-solute system to gather any meaningful data.
> The density of the system is a property dominated by the water model.  I am also 
> unsure of the validity of G96 parameters (but you haven't said which parameter 
> set, "ffG3a" is not real) when combined with TIP4P.  The Gromos force fields 
> were parameterized with SPC; TIP4P is more often used with OPLS.  I don't know 
> exactly what effect that will have, but you should probably at least be using a 
> robust combination, or demonstrate somehow that your application of the force 
> field/water model is correct.
> -Justin
> > Looking forward to hearing from you
> > neal
> > 
> > 
> > 
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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