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On 16/10/2011 6:12 AM, Broadbent, Richard wrote:
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cite="mid:CABF99A9.2C0F%25richard.broadbent09@imperial.ac.uk"
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<title>Re: [gmx-users] how to calculate the normal of plane for
Tryptophan or how to get the comparison matrix in g_rms</title>
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Have you thought about using the cross product. If you took
the cross product of the unit vector in the direction of every
atom starting from atom 1 then moved on to starting from atom
2 and so on you would have a set of vectors normal to every
group of three atoms. If you then normalised them and defined
one to be pointing upwards you could then ensure using dot
products that they all pointed the same way, a condition like
if a.b <0 b=-b would probably work you could then take the
mean of the vectors. This should give an average normal vector
to the plane of the molecule. <br>
<br>
If you’re going to be doing this a lot I would suggest
removing the inherent double counting (r12=-r21).<br>
<br>
You could also think about weighting normal vectors in the
averaging, for instance you could do it based on the sine of
the angle between the vectors which generated them, or the
mass of the atoms (H’s will more out of plane than carbons
typically)<br>
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Calculating the principle axes of inertia is a better approach.
There's a GROMACS tool that does it.<br>
<br>
Mark<br>
<br>
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cite="mid:CABF99A9.2C0F%25richard.broadbent09@imperial.ac.uk"
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<br>
Hope that’s helpful<br>
<br>
Richard<br>
<br>
On 15/10/2011 15:45, "xiaodong huang" <<a
moz-do-not-send="true" href="xiaodonghuang2060@gmail.com">xiaodonghuang2060@gmail.com</a>>
wrote:<br>
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<blockquote><font face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size:11pt">I send this message yesterday, but I
myself donot see this message, so, I send it again, very
sorry for the spam.<br>
Dear gmxer's<br>
I am simulating a protein, want to calculate the normal of
plane for Tryptophan residue amino acid in that protein.<br>
We need to take into account that, in simulation, atoms of
TRP vibrate all the time, and they are not always on the
same plane:<br>
If they were on the same plane in my simulation, to
calculate the normal would be rather straighforward.<br>
As those atoms are not on the same plane, I think my
calculation should be something like least square fitting. I
look at g_rms command,<br>
and plan to calculate the normal in following steps:<br>
1. create a Tryptophan with ideal configuration, where all 8
C atom and N atom (except CB atom) should be in the same
plane,<br>
I put these 9 atoms in xy plane, and the normal of this
TRP molecule is just z axis<br>
2.I then calculate the rms between the TRP residue in my
simulation and that ideal TRP molecule<br>
3.If I know the rotate matrix (e.g. how to rotate the TRP in
my simulation in the least-squares fitting of rms
calculation), then I<br>
just rotate z axis (0,0,1) back ( in other words,
multiple z axis (0,0,1) with the inverse of that rotate
matrix) to get the plane normal<br>
for TRP in my simulation.<br>
So, I am wondering how to know the the rotate matrix when
g_rms do the least-squares fitting? Is that in the
comparison matrix<br>
dumped by the -bin option? If so, how to read the rotate
matrix from that binary file produced by -bin option?<br>
Or, if there is other way that I can calculate plane normal
for TRP?<br>
Thank you so much for your kind help.<br>
yours<br>
xiaodong<br>
school of chem, ANU<br>
<br>
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