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

[Berk Hess]

It seems you are right.
The density is calculated a few lines before 1/visc is stored, but it is not being used.
Strange that this always went unnoticed, since it already seems to have been wrong in 4.0.
The density of water is so close to 1000 that you wouldn't notice the difference 

But in a quick test I don't get the correct viscosity either way.
I will have to find time for a thorough check.
Do you get the right answer by dividing by the missing density term in src/mdlib/mdebin.c?

Berk

Date: Wed, 19 Jan 2011 14:48:32 -0600
From: xiaohuli914 at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] RE: Important: Bugs in NEMD calculation



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"









> 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

> --

> gmx-users mailing list    gmx-users at gromacs.org

> http://lists.gromacs.org/mailman/listinfo/gmx-users

> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

> Please don't post (un)subscribe requests to the list. Use the

> www interface or send it to gmx-users-request at gromacs.org.

> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-------------- next part --------------

An HTML attachment was scrubbed...

URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110119/1ffc9f59/attachment.html




------------------------------



--

gmx-users mailing list

gmx-users at gromacs.org

http://lists.gromacs.org/mailman/listinfo/gmx-users

Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!



End of gmx-users Digest, Vol 81, Issue 127

******************************************





-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110119/78703d32/attachment.html>