How to write trajectory out to a file and visualize in VMD

[ashan dayananda]

Hello,

I am new to use MDAnalysis and I would like to know how can I write the PC outputs as in dcd format or combined pdb format so I can view in VMD.

Appreciate your help.

Thanks,

Ashan. 

[Oliver Beckstein]

Hi Ashan,

Welcome to the MDAnalysis user list!

The user guide has a section on PCA https://userguide.mdanalysis.org/stable/examples/analysis/reduced_dimensions/pca.html; at the bottom it shows how to create a  universe proj1 with a PCA-filtered trajectory. You can write out this trajectory to a DCD with

proj1.atoms.write(“pca1.pdb”)

proj1.atoms.write(“pca1.dcd”, frames=“all”)

and then use the PDB and DCD file in VMD.

Oliver

p.s.: There’s also a more explicit way to write a trajectory:

with MDAnalysis.Writer(“pca1.dcd”, n_atoms=proj1.atoms.n_atoms) as W:

       for ts in proj1.trajectory:

              W.write(proj1.atoms)

   

--

Oliver Beckstein (he/his/him)

orbe...@gmail.com

[ashan dayananda]

Hi Oliver,

That makes sense. It worked.

Thank you,

Ashan.

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