Normal vector

[Ondrej Kroutil]

Hi Plumed users,
Sorry for this probably simple question but I cannot find solution: can I somehow define normal vector (crossproduct) of two vectors (distances)?
Namely, I have cisplatin molecule and need to define normal to plane defined by Pt-N1 and Pt-N2 vectors.

Thanks a lot for any reply.

    Ondřej Kroutil

[Gareth Tribello]

You can use this:

http://plumed.github.io/doc-master/user-doc/html/_p_l_a_n_e_s.html

Gareth

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[Ondrej Kroutil]

Dear Gareth,
Thanks a lot for reply. I have noticed this function but it requires special compilation of the Plumed (or CP2K with Plumed in my case) with crystallization module and I take it as a very last option.
Please, does anybody have other solution of this problem???

Thank you.

    OK

[Giovanni Bussi]

Check GHOST then ANGLE. Alternatively, use MATHEVAL

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[Ondrej Kroutil]

Hi,
  I have just discovered my old post and I have to say that I have solved the problem with the normal to surface using Giovanni's hint:
  So, here is my input if someone need it (Plumed2). It's made for cisplatin (https://en.wikipedia.org/wiki/Cisplatin)...

****************
gh: GHOST ATOMS=1,2,3 COORDINATES=0,0.5,0   # atoms 1,2,3 define plane, in my case atoms Pt, N1 and N2 in cisplatin molecule, one GHOST atom is product
dist: DISTANCE ATOMS=1,4 NOPBC  # defines vector between Pt and Cl1 in cisplatin
ang: ANGLE ATOMS=4,1,gh  # defines angle between normal to the plane and Pt-Cl1 vector

DUMPATOMS STRIDE=1 FILE=file.gro ATOMS=1,2,3,4,5,gh  # just to see in VMD how it works

****************
Thanks for PLUMED guys.

    OK

[Lakshman Verma]

Hi Ondrej,

I am trying to calculate a normal to my approximate planer molecule and then restrain the angle between that normal and z-axis. 

I have not been able to fully understand how Ghost Atoms work. In particular, I am not able to understand what COORDINATES I need to provide. 

I would like to have a respective normal to the molecule plane, which is free to rotate, at every time step. 

Any help would be appreciated.

Thanks

Lakshman 

[Brian Wiley]

Hi OK,

 When you say this in the comment “one GHOST atom is product” do you mean cross-product, i.e. the cross product of the two vectors made by the three atoms which would be the normal.  Also why do you have a 0.5 for the y in COORDINATES?

Brian