On 2011-04-27 17.58, Xiaohu Li wrote:
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Message: 4
Date: Wed, 27 Apr 2011 08:24:52 +0200
From: David van der Spoel <sp...@xray.bmc.uu.se>
Subject: Re: [gmx-users] BUG in angular removal part??
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4db7b6b4.5090...@xray.bmc.uu.se>
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On 2011-04-26 19.38, Xiaohu Li wrote:
Hi, gromacs developers,
It seems that there is a bug regarding the angular moment removal. This
may not be very important for many users since most of them are doing
PBC where it is irrelevant, but if you are doing cluster or if you
really care the angular momentum like I
do(I want the angular momentum to be exactly zero since this corresponds
to some quantum resolved state), then it is important.
The angular momentum removal part in mdlib/vcm.c where it evaluate
moment of inertia is wrong, subroutine *update_tensor.
*Specifically, the diagonal part is not calculated right. According to
either */Classical Mechancs, by Goldstein or Theoretical Mechanics of
Particles and Continua, by A.L.Fetter and J.D.Walecka.
I_{xx}=\sum_{i} m_{i}*(r_{i}^2-x_{i}^2), where x can be x,y,z.
But the /**update_tensor gives
**/I_{xx}=\sum_{i} m_{i}*(x_{i}^2).
/*/I initially thought there could be some other routine to correct
update_tensor, but apparently, it is calculated according to that, and I
manually calculated them and turns out my theory is right, the
update_tensor is wrong as it stands.
/Again, this would not affect, say, 99.999% of the user, but it will
always be good to have a clean code.
Thanks
I found the eqn. in Goldstein p 195. I guess this takes care of the
center of mass contribution. So if you center your system in the
origin at time zero the present code should still work. However, we
really should subtract the center of mass.
Mine certainly does not say the same thing. I'm using an older version
of Goldstein by Addison-Wesley, 1950, seventh printing. Chapter 5, the
third page, Eqn. 5-6 and 5-7. This does not match the code in gromacs.
Yes, I filed a redmine issue so as not to forget it for the next
release. Nevertheless, the you can use the existing code by centering
your molecule on the origin (I think). If you can fix the code yourself
you could send me a patch too.
/
/Xiaohu/
/
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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