[gmx-users] Important: Bugs in NEMD calculation

[David van der Spoel]

On 2011-01-19 20.43, Berk Hess wrote:
>
>
>  > Date: Wed, 19 Jan 2011 19:13:12 +0100
>  > From: spoel at xray.bmc.uu.se
>  > To: gmx-users at 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!

But the volume of a triclinic box is the determinant of the box (maybe 
less than the product of the XX YY ZZ).

>
> 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.
>  > spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>  > --
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se