How to cut the trajectory of an universe at given times and use it in a radial distribution function analysis and similar?

[Elías C]

Dear researchers,

I am working with an xtc file obtained from gromacs. It has 3000 frames, in total 30 ns, I would like to use the data from the first 10 ns to perform a RDF analysis. I have read about how to cut a trajectory with MDAnalysis but I don't understand how to integrate the method in a type of analysis for which, a for loop is not commonly used.

Thank you for reading.

[Ropon-Palacios G.]

a common way would be for you to select the number of frames you want to use

 

u.traj [0: 1000]

 

this could select the first 1000 frames.

in your case it would be [0: 10000], the first 10,000.

 

To un loop can use:

for i in u.traj[0:10000]:

do anything

 

 

Best,

 

Geo.

 

From: <mdnalysis-...@googlegroups.com> on behalf of Elías C <ecoba...@gmail.com>
Reply-To: <mdnalysis-...@googlegroups.com>
Date: Monday, September 13, 2021 at 9:53 PM
To: <mdnalysis-...@googlegroups.com>
Subject: [mdnalysis-discussion] How to cut the trajectory of an universe at given times and use it in a radial distribution function analysis and similar?

 

Thank you for reading.

[Hugo Macdermott-Opeskin]

Hi,

You can use the `start, stop step` keywords to slice the trajectory for analysis.

For example 

`

import MDAnalysis as mda

u = mda.Universe(my_topology, my_trajectory)

ag1 = u.select("group1")

ag2 = u.select("group2")

rdf = mda.analysis.rdf.InterRDF(ag1, ag2, start=0, stop=1000, step=1)

rdf.run()

`

[Elías C]

Thank you. It was very simple. I am very grateful.

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