[gmx-users] defined least squares plane

David van der Spoel spoel at xray.bmc.uu.se
Sun Jan 6 18:52:23 CET 2002

On Sat, 5 Jan 2002 nicolis at guideo.fr wrote:

>I am also interested for the answer.
>I wanted to measure the angle between two phenyl rings and I only
>managed to define two 3-atom planes, one for each ring, and follow this
>angle with g_sgangle. I repeated with different sets of 3-atoms to have
>various estimations of the variations, but of course it is not as
>satisfactory as a least square plane computed from the 6 atoms of the
>On the other hand, if it is not included in the programs it should not
>be very complicated to program. All the coordinates are in the .trr? I
>see the formulaes to use given the xyz of the atoms but I did not yet
>looked at the manual to see how to access the xyz's.

I suggest you have a look at the source code for g_sgangle, there you can
find how three atom planes are defined based on the coordinates. It
shouldn't be too hard to add support for six (and five) rings. 

On the other hand, the results will differ only marginally and on average
probably not at all. Nevertheless, if either of you is willing to
implement and test it, I'll be happy to put it into the next official

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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