> Date: Wed, 19 Jan 2011 20:43:20 +0100 > From: Berk Hess <[email protected]> > Subject: RE: [gmx-users] Important: Bugs in NEMD calculation > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Date: Wed, 19 Jan 2011 19:13:12 +0100 > > From: [email protected] > > To: [email protected] > > Subject: Re: [gmx-users] Important: Bugs in NEMD calculation > > > > On 2011-01-19 18.36, Xiaohu Li wrote: > > > Hi, All, > > > I've found a bug in the NEMD calculation for viscosity. This has > > > been reviewed in /*Hess's paper at JCP 116 209 2002.*/ > > > The version of gromacs I'm using is the development version. > > > Notice that this version correct a previous but of 4.5.3, where you > uses > > > NEMD, both the term V(eq. 21 on Hess's paper) and 1/eta(shear viscosity > > > inverse) are supposed to be written to the *.edr file, however, > > > the 4.5.3 versions does not have this. This version can be retrieved at > > > > http://repo.or.cz/w/gromacs.git/commit/c83de86d65ce7135be6cef15e9100d7516e6d9a7 > > > *However, even this version is buggy since eta=A*rho/(V*k**2)(eq. 20 > > > Hess's paper)*. *I have performed simulation and has found out that the > > > V and eta which are written in *edr file does not match according to > the > > > formula, a little further check on the source code mdebin.c under the > > > directory src/mdlib shows that it is actually calculating > > > eta=A*Volume/(V*k**2) where density of rho should have been used. (This > > > is at line 755 of mdebin.c ). > > > I hope everyone who is using this can be aware of this, if you > ever > > > used this code to produce data, the V is correct from *edr, however, > you > > > need to manuelly get your eta using the above formula. > > > For the GMX developers, I hope anyone of you can correct this bug. > > > > > I fixed this bug recently is the git release-4-5-patches branch. > You can get the fix from git and it will be in the 4.5.4 release > (no date yet). > Which one are you referring to? The one I got is the one you uploaded that fixed the zero viscosity and 2*cosZ*vel-x in edr file. This bug refers the wrong calculation of 1/eta.
> > > Thanks for pointing that out. There also is a small issue in that the > > volume is computed for a rectangular box > > vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ]; > > dens = (tmass*AMU)/(vol*NANO*NANO*NANO); > > > > which would be incorrect for a non-rectangular box. You should however > > use a rectangular box for this kind of calculations, although this is > > not enforced by grompp. > > No. > That formula is correct for any triclinic box! > > Berk > > > > > > > > > > > > Xiaohu > > > * > > > > > > > > > -- > > David van der Spoel, Ph.D., Professor of Biology > > Dept. of Cell & Molec. Biol., Uppsala University. > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > > [email protected] http://folding.bmc.uu.se > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110119/1ffc9f59/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 81, Issue 127 > ****************************************** >
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
