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crest-lab / crest

CREST - A program for the automated exploration of low-energy molecular chemical space.
https://crest-lab.github.io/crest-docs/
GNU Lesser General Public License v3.0
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unable to read crest_dynamics.trj #362

Open Artaious opened 5 days ago

Artaious commented 5 days ago

I'm making my first steps with crest, mainly following the firsts examples in the documentation webpage. I start by getting the alanineglycine geomtry from the there (https://crest-lab.github.io/crest-docs/page/examples/example_1.html) and running crest in the terminal by crest struc.xyz --gfn2 --gbsa h2o -T 4

After crest terminates normaly, I would like to visualize the dynamics within the crest_dynamics.trj. My issue is that neither with vmd nor with pymol I'm able to do so, getting an error when trying to load the trj file.

Pymol proecedure: load struc.xyz

and then: load_traj crest_dynamics.trj

Which gives the following error --> ObjMolLoadTRJFile-Error: Failed to read expected coordinate value. This traj. does not match the loaded parameter/topology file. Likely cause: either the atom count or the periodic box settings are inconsistent between the two files.

crest_dynamics.txt struc.txt (change the termination of the file to make possible its upload).

Anyhelp or comment will be greatly appreciated! Greetings.

pprcht commented 5 days ago

The file ending .trj is likely preoccupied in most visualization programs, we are keeping it around due to legacy purposes, which is a bit unfortunate, but the file is really just a plain .xyz. In other words, if you rename the file to crest_dynamics.trj.xyz you should be able to open it just fine.

Artaious commented 15 hours ago

The file ending .trj is likely preoccupied in most visualization programs, we are keeping it around due to legacy purposes, which is a bit unfortunate, but the file is really just a plain .xyz. In other words, if you rename the file to crest_dynamics.trj.xyz you should be able to open it just fine.

Hello everyone, Sorry for the delay. I wanted to do a few trials before ansewring. It works as you said. Just by changing the name and using the trial version of ChemCraft I was able to visualise the dynamics and get what I needed.

Thank you very much for your prompt reply. Regards.