> Date: Wed, 19 Jan 2011 19:13:12 +0100 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > 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). > 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. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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