[gmx-users] Important: Bugs in NEMD calculation

Xiaohu Li xiaohuli914 at gmail.com
Wed Jan 19 18:36:06 CET 2011

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
     *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.

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