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<br><br>> Date: Wed, 19 Jan 2011 20:52:13 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Important: Bugs in NEMD calculation<br>> <br>> On 2011-01-19 20.43, Berk Hess wrote:<br>> ><br>> ><br>> > > Date: Wed, 19 Jan 2011 19:13:12 +0100<br>> > > From: spoel@xray.bmc.uu.se<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] Important: Bugs in NEMD calculation<br>> > ><br>> > > On 2011-01-19 18.36, Xiaohu Li wrote:<br>> > > > Hi, All,<br>> > > > I've found a bug in the NEMD calculation for viscosity. This has<br>> > > > been reviewed in /*Hess's paper at JCP 116 209 2002.*/<br>> > > > The version of gromacs I'm using is the development version.<br>> > > > Notice that this version correct a previous but of 4.5.3, where you<br>> > uses<br>> > > > NEMD, both the term V(eq. 21 on Hess's paper) and 1/eta(shear viscosity<br>> > > > inverse) are supposed to be written to the *.edr file, however,<br>> > > > the 4.5.3 versions does not have this. This version can be retrieved at<br>> > > ><br>> > http://repo.or.cz/w/gromacs.git/commit/c83de86d65ce7135be6cef15e9100d7516e6d9a7<br>> > > > *However, even this version is buggy since eta=A*rho/(V*k**2)(eq. 20<br>> > > > Hess's paper)*. *I have performed simulation and has found out that the<br>> > > > V and eta which are written in *edr file does not match according<br>> > to the<br>> > > > formula, a little further check on the source code mdebin.c under the<br>> > > > directory src/mdlib shows that it is actually calculating<br>> > > > eta=A*Volume/(V*k**2) where density of rho should have been used. (This<br>> > > > is at line 755 of mdebin.c ).<br>> > > > I hope everyone who is using this can be aware of this, if you ever<br>> > > > used this code to produce data, the V is correct from *edr,<br>> > however, you<br>> > > > need to manuelly get your eta using the above formula.<br>> > > > For the GMX developers, I hope anyone of you can correct this bug.<br>> > > ><br>> ><br>> > I fixed this bug recently is the git release-4-5-patches branch.<br>> > You can get the fix from git and it will be in the 4.5.4 release<br>> > (no date yet).<br>> ><br>> > > Thanks for pointing that out. There also is a small issue in that the<br>> > > volume is computed for a rectangular box<br>> > > vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];<br>> > > dens = (tmass*AMU)/(vol*NANO*NANO*NANO);<br>> > ><br>> > > which would be incorrect for a non-rectangular box. You should however<br>> > > use a rectangular box for this kind of calculations, although this is<br>> > > not enforced by grompp.<br>> ><br>> > No.<br>> > That formula is correct for any triclinic box!<br>> <br>> But the volume of a triclinic box is the determinant of the box (maybe <br>> less than the product of the XX YY ZZ).<br><br>Gromacs only allows boxes with the upper (or lower depending on how you<br>order the elements) triangle zero. This means the determinant is equal<br>to the product of the diagonal elements. This product is (slighlty) more accurate<br>and computationally less expensive than calling the det function.<br><br>Berk<br><br>> <br>> ><br>> > Berk<br>> ><br>> > ><br>> > > ><br>> > > ><br>> > > > Xiaohu<br>> > > > *<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.<br>> > > spoel@xray.bmc.uu.se 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<br>> > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists<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.<br>> spoel@xray.bmc.uu.se 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/Support/Mailing_Lists/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/Support/Mailing_Lists<br> </body>
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