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.
Emails:
mohamed_marzouk.sci.asu.edu.eg
marzouk.aa.m.titech.ac.jp
marzouk_biophysics.yahoo.com
mohamedmarzoukphysics.gmail.com
Mob. and WhatsApp.:
+81 070-4070-9549
+2 01061417414
> On Jun 2, 2020, at 4:26 AM, Daniel Roe <daniel.r.roe.gmail.com> 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
