Re: [AMBER] COM position

From: mohamed marzouk <>
Date: Wed, 3 Jun 2020 08:48:06 +0900

Thank you 🙏 now very clear.
I am most grateful Daniel
Best regards,
Mohamed Marzouk Sobeh
Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
T.A Physics department,Ain Shams University, Cairo, Egypt.

Mob. and WhatsApp.:
               +81 070-4070-9549
                +2 01061417414

> On Jun 2, 2020, at 4:26 AM, Daniel Roe <> wrote:
> Hi,
> 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
> coordinates.
> 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':
> [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,
> -Dan
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Received on Tue Jun 02 2020 - 17:00:02 PDT
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