<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Date: Wed, 19 Jan 2011 20:43:20 +0100<br>
From: Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>><br>
Subject: RE: [gmx-users] Important: Bugs in NEMD calculation<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <COL113-W2019E7174AFFBAEF819A1A8EF60@phx.gbl><br>
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> Date: Wed, 19 Jan 2011 19:13:12 +0100<br>
> From: <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>
> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Subject: Re: [gmx-users] Important: Bugs in NEMD calculation<br>
><br>
> On 2011-01-19 18.36, Xiaohu Li wrote:<br>
> > Hi, All,<br>
> > I've found a bug in the NEMD calculation for viscosity. This has<br>
> > been reviewed in /*Hess's paper at JCP 116 209 2002.*/<br>
> > The version of gromacs I'm using is the development version.<br>
> > Notice that this version correct a previous but of 4.5.3, where you uses<br>
> > NEMD, both the term V(eq. 21 on Hess's paper) and 1/eta(shear viscosity<br>
> > 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" target="_blank">http://repo.or.cz/w/gromacs.git/commit/c83de86d65ce7135be6cef15e9100d7516e6d9a7</a><br>
> > *However, even this version is buggy since eta=A*rho/(V*k**2)(eq. 20<br>
> > Hess's paper)*. *I have performed simulation and has found out that the<br>
> > 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<br>
> > directory src/mdlib shows that it is actually calculating<br>
> > eta=A*Volume/(V*k**2) where density of rho should have been used. (This<br>
> > is at line 755 of mdebin.c ).<br>
> > I hope everyone who is using this can be aware of this, if you ever<br>
> > used this code to produce data, the V is correct from *edr, however, you<br>
> > 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>
I fixed this bug recently is the git release-4-5-patches branch.<br>
You can get the fix from git and it will be in the 4.5.4 release<br>
(no date yet).<br></blockquote><div>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.<br>This bug refers the wrong calculation of 1/eta.<br>
<br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
> Thanks for pointing that out. There also is a small issue in that the<br>
> volume is computed for a rectangular box<br>
> vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];<br>
> dens = (tmass*AMU)/(vol*NANO*NANO*NANO);<br>
><br>
> which would be incorrect for a non-rectangular box. You should however<br>
> use a rectangular box for this kind of calculations, although this is<br>
> not enforced by grompp.<br>
<br>
No.<br>
That formula is correct for any triclinic box!<br>
<br>
Berk<br>
<br>
><br>
> ><br>
> ><br>
> > Xiaohu<br>
> > *<br>
> ><br>
><br>
><br>
> --<br>
> David van der Spoel, Ph.D., Professor of Biology<br>
> Dept. of Cell & Molec. Biol., Uppsala University.<br>
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
> <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
> --<br>
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