[gmx-users] center of mass removal

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Mar 19 08:20:41 CET 2008

Hi baloilguillare at interfree.it,

I have recently modified the routine as to not crash upon a shift over
periodic boundaries, which would occur with the original code. Also, I
streamlined the routines such that they don't lead to large
modifications of update.c
I will put the modified code on line, probably today, and provide the
link to it. This concerns version 3.3.1.
I'm working on making the implementation more robust, and if finished
I'll short-circuit with David about adding the changes to the official



On Wed, Mar 19, 2008 at 12:22 AM,  <baloilgiullare at interfree.it> wrote:
> Hi all,
>  searching in the ml I found this thread:
>  http://www.gromacs.org/pipermail/gmx-users/2006-April/021256.html
>  about comm-mode=angular and the method described in
>  J. Chem. Phys. 112(1) pp. 9-23 to remove com translation and rotation.
>  I was not able to download the modified versions of the code at
>  http://md.chem.rug.nl/~tsjerk/GMX/ where this method is implemented.
>  I was wondering if anyone has implemented it in some newer version of
>  gromacs as Tsjerk Wassenaar did for 3.2.1.
>  I am reading the relevant paper about the method just now but Iwas not
>  able to find any additional examples of its use.
>  When it is better/necessary to use it than simply removing com
>  translation, given that I do not want to use comm-mode=angular with
>  pbc?
>  thank in advance
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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