slicing by distance

[hanahg]

Hi,

I would like to slicing a trajectory by distance, is it possible?

[IAlibay]

@hanahg this seems to be more of a usability question so I will convert this to a discussion item rather than an issue.

[IAlibay]

@hanahg Could you offer more details about what you are trying to do? Specifically, what do you mean by "distance"?

[hanahg]

In fact, I should calculate and draw a curve of electrostatic charge of a Nan-oparticle(NP). For that I should calculate the charge of NP from the center, then calculate the electrostatic charges(as it reported in a paper). I don't know how but maybe by calculating charge of each slice as a group.

[orbeckst]

If you can formulate your problem in terms of equations then we can help you and tell you how you can implement the equations with MDAnalysis.

If you only have a vague idea that are expressed in words then we might just not have any idea how to help and then you might not get any replies. The more precise and focused your question is, the more likely it's generally that someone can help.

[hanahg]

I have explained "I should calculate and draw a curve of electrostatic charge of a Nan-oparticle(NP). For that I should calculate the charge of NP from the center, then calculate the electrostatic charges".
please tell me how to calculate distance of atoms from the center of Nanoparticle, I mean position (0 0 0)

[RMeli]

I have explained

@hanahg if someone asks for additional explanation, it is likely because they did not understand what you want to do. It is unclear to me what you are trying to achieve from your explanation.

please tell me how to calculate distance of atoms from the center of Nanoparticle, I mean position (0 0 0)

What do you mean by position (0, 0, 0)? If your nanoparticle is centred at the origin, then the distance of atoms from the center, will be the distance of the atoms from the origin. If you have an atom group ag, you can get the position of all the atoms as a NumPy array with ag.positions.

If the nanoparticle is not actually centred at the origin, you can select the nanoparticle using select_atoms and compute its center of mass with center_of_mass() or its center of geometry with center_of_geometry().

See User Guide - AtomGroup positions and methods for some more details.