[gmx-users] Important: Bugs in NEMD calculation

[Berk Hess]

> 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!

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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