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<br><br>> Date: Wed, 24 Feb 2010 14:46:17 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] density<br>> <br>> On 2/24/10 2:00 PM, Sander Pronk wrote:<br>> > You got pretty close to what the density of SPC water is at 298K<br>> ><br>> > According to "Temperature dependence of TIP3P, SPC, and TIP4P water from<br>> > NPT Monte Carlo simulations: Seeking temperatures of maximum density",<br>> > William L. Jorgensen, Corky Jenson, J. Comp. Chem, Volume 19 Issue 10,<br>> > Pages 1179 - 1186 (1998)<br>> > it should be 0.985g/ml, and TIP4P will give you 1.001g/ml.<br>> ><br>> > Remember that you're simulating SPC water, not real water.<br>> ><br>> <br>> Correct, but note that<br>> 1. Jorgensen uses a funky switch function rather than PME (undocumented, <br>> except in my paper JCTC 2 [2006] p. 1)<br>> 2. Monte Carlo iso MD (although that shouldn't make a difference)<br><br>Well, this does make a difference if some interactions are not switched.<br>MC will see the jump in the potential at the cut-off, whereas MD which<br>samples according to the forces does not.<br><br>Berk<br><br>> 3. Long range corrections to the energy, but not to the pressure<br>> in case you want to reproduce his results :).<br>> <br>> Cheers, David,<br>> <br>> > Sander<br>> ><br>> ><br>> ><br>> > On Feb 24, 2010, at 13:23 , Sunil Thapa wrote:<br>> ><br>> >> Respectable Experts<br>> >> Grettings<br>> >> I am studying diffusion of an oxygen molecule in 255 molecule of SPC<br>> >> water. I need to determine diffusion coefficient at temperature 298 K<br>> >> and 1 atm pressure. In order to do that<br>> >> using editconf I scaled the density of the system including oxygen to<br>> >> 1g/l. I checked the density after energy minimization (steepest<br>> >> descent) which gave the reading of 0.76 g/l. After that I equilibrated<br>> >> the system to pressure of 1 bar and temperature of 298 K using NPT<br>> >> simulation (berendsen). The density reading was 0.98. When I checked<br>> >> the density table at 298 K, it was about 0.9927 g/l.<br>> >> I am afraid if my density is not consistent with experimental density<br>> >> of the system. Is this some bug of gromacs 3.2.1 or my understanding<br>> >> of thermodynamics is very poor for pressure and liquid density. Please<br>> >> help me on this.<br>> >> Should I use the same NPT simulation to derive the experimental<br>> >> diffusion coefficient ?<br>> >> Looking forward to hearing from you<br>> >> Neal, Nepal<br>> >><br>> >><br>> >> --<br>> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> <mailto: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>> <br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone:        +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se        spoel@gromacs.org http://folding.bmc.uu.se<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: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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