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Hi,<br><br>I would think this is one of very few examples where most of the force field is quite<br>uncritical. Diffusion of a hydrophobic solute in water will mainly depend on the size<br>of the solute and the diffusion coefficient of the water model itself.<br>Of the common water models, SPC/E has the best diffusion coefficient and it<br>combines well with the Gromos force fields, so use that.<br><br>It is well known that the diffusion of SPC is twice what it should be.<br><br>Berk<br><br><br>> Date: Wed, 10 Mar 2010 07:35:41 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] diffusion coefficient of oxygen<br>> <br>> <br>> <br>> Sunil Thapa wrote:<br>> > Respected Experts<br>> > <br>> > I need your help<br>> > <br>> > In my study of diffusion of a oxygen molecule in 255 molecules of water, <br>> > I previously used SPC water model with ffgmx force field with cutoff L-J <br>> > and Coulomb interaction. I wanted to reproduce the experimental value <br>> > 2.4 unit for diffusion coefficient of oxygen in water at 298 K and 1 atm.<br>> > <br>> > To equilibrate the system to the experimental water density of 997 I <br>> > used Berendsen thermostat and the same barostat. The density of the <br>> > system was 980(+-) 10 kg/m3 which is not the experimental value. After <br>> > equilibration, I subjected the system to NVT ensemble md of 100 ns. I <br>> > got the msd for oxygen molecule and analyzing first 4 ns (which was a st <br>> > line part) of the plot, I got the diffusion coefficient of about 2.45 <br>> > unit which is close to the experimental value. The question is how can <br>> > the diffusion coefficient be so close when density is not produced. Is <br>> > this a mere coincidence?<br>> > <br>> <br>> More likely a consequence of the water model itself. Keep in mind that SPC <br>> water is not real water, it does not reproduce all properties of water <br>> accurately. No water model does. Look into the literature for the expected <br>> density of SPC, but 980 does sound close to what is expected.<br>> <br>> > Thinking that I used TIP4P water model with the same number but <br>> > different force field ffG3a<br>> > . I equilibrated the system to the same pressure and temperature with <br>> > the same algorithms. After equilibration, the correspondng density was <br>> > 991(+-) 15 kg/m3. Then I subjected it to the production run of 100ns. <br>> > Now what I see is that the MSD curve is a hill, initially increasing, <br>> > reaching maximum and again returning to the base. The diffusion <br>> > coefficient is 0.7 unit for 100 ns of trajectory.<br>> > <br>> > What would have happened? Is this due to the increased density? Your <br>> > precious knowledge on the subject matter would give me a sigh of relief.<br>> > <br>> <br>> You must be careful interpreting your results. If you only have one molecule of <br>> your solute, then statistics will likely be very poor. You probably need either <br>> more solute molecules within a given system or many replicates of the same <br>> single-solute system to gather any meaningful data.<br>> <br>> The density of the system is a property dominated by the water model. I am also <br>> unsure of the validity of G96 parameters (but you haven't said which parameter <br>> set, "ffG3a" is not real) when combined with TIP4P. The Gromos force fields <br>> were parameterized with SPC; TIP4P is more often used with OPLS. I don't know <br>> exactly what effect that will have, but you should probably at least be using a <br>> robust combination, or demonstrate somehow that your application of the force <br>> field/water model is correct.<br>> <br>> -Justin<br>> <br>> > Looking forward to hearing from you<br>> > neal<br>> > <br>> > <br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />New Windows 7: Simplify what you do everyday. <a href='http://windows.microsoft.com/shop' target='_new'>Find the right PC for you.</a></body>
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