Hi, All,<br> I've found a bug in the NEMD calculation for viscosity. This has been reviewed in <i><b>Hess's paper at JCP 116 209 2002.</b></i><br> 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,<br>
the 4.5.3 versions does not have this. This version can be retrieved at<br><a href="http://repo.or.cz/w/gromacs.git/commit/c83de86d65ce7135be6cef15e9100d7516e6d9a7">http://repo.or.cz/w/gromacs.git/commit/c83de86d65ce7135be6cef15e9100d7516e6d9a7</a><br>
<b>However, even this version is buggy since eta=A*rho/(V*k**2)(eq. 20 Hess's paper)</b>. <b>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 <br>
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 ).<br>
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.<br> For the GMX developers, I hope anyone of you can correct this bug.<br>
<br><br><br>Xiaohu<br></b>