[gmx-users] RE: Important: Bugs in NEMD calculation

[Xiaohu Li]

> Date: Wed, 19 Jan 2011 20:43:20 +0100
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] Important: Bugs in NEMD calculation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <COL113-W2019E7174AFFBAEF819A1A8EF60 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
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>
> > 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).
>
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.
> > spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> > --
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