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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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initial structures #193

Closed gpwood closed 5 months ago

gpwood commented 1 year ago

This is more a question on how crest works than it is an issue. If you have a standard call like: crest struc.xyz --gfn2 --gbsa h2o -T 4 Do the xyz coordinates as given in "struc.xyz" get used as a starting point (seed) for the rotamer->meta-dynamics workflow? If it is used as a seed structure, is it possible to have multiple xyz coordinates in that file to initiate the workflow? Or would I have to do start them all separately?

Thanks!

pprcht commented 1 year ago

Hi, the struc.xyz is the starting point for the search, but it is not explicitly included as a metadynamics bias. These are taken from the simulation itself. If there is more than one structure in the struc.xyz only the first one should be read by the program. If you would like to use different starting points, scripting it and running separate jobs would be the way to go, as you correctly suggested. This will also be much quicker, e.g. if you work on a cluster and can submit the jobs separately. Pasting the final ensemble files into one and running CREGEN afterwards is then easy.

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