Re: [AMBER] COM position

From: Daniel Roe <>
Date: Mon, 1 Jun 2020 15:26:00 -0400


So I think that the manual is actually helpful here. From the manual entry
for the cpptraj 'vector' command:

[out <filename>] Write vector data to <filename> with format ’Vx Vy Vz Ox
Oy Oz’ where V denotes vector coordinates and ’O’ denotes origin

So the first 3 numbers are the actual vector. For 'vector mask' which is
"Store vector from center of mass of atoms in <mask1> to atoms in
<mask2>.", you are calculating XYZ(mask2) - XYZ(mask1), where XYZ(mask) is
the coordinates of the center of mass of atoms selected by <mask>. The
second three numbers are the origin. In this case, the center of mass of
atoms in <mask1>. This is why the first 3 columns in the output from your
second vector command (which only requests the center of mass of residues
1-199) matches the origin of your first vector command. As for

[ptrajoutput] Write vector data in ptraj style (Vx Vy Vz Ox Oy Oz Vx+Ox
Vy+Oy Vz+Oz).

So the last 3 numbers are the real Cartesian coordinates of the vector
"head" (with the "tail" being the origin).

Hope this helps,

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Received on Mon Jun 01 2020 - 12:30:03 PDT
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