Difference between revisions of "Crest"

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m (and another fix..)
m (Fixing typos, minor reformulations.)
 
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More advanced syntax looks like this:
 
More advanced syntax looks like this:
  cnorris@lilo7:~$ Crest structure.xyz -chrg 1 -quick
+
  cnorris@lilo7:~$ Crest structure.xyz -chrg 1 -uhf 0 -quick
Here I've added quick keywords which makes the screening less in-depth but it goes much quicker. And also chrg keyword to define charge. There is also keyword for spin and many more. For more detailed description please refer to crest [https://xtb-docs.readthedocs.io/en/latest/crestcmd.html crest command line arguments documentation].
+
Here I've added quick keyword which makes the screening less in-depth but it goes much quicker. I also added chrg keyword to define charge and uhf keyword to define spin state. For more detailed description and full list of keywords, please refer to [https://xtb-docs.readthedocs.io/en/latest/crestcmd.html crest command line arguments documentation].
  
 
==Processing calculations==
 
==Processing calculations==
Once calculation is finished, conformers list and best structure from crest structure pool is received. There is also folder where rotamers and other things are stored.
+
Once calculation is finished, conformers list and best structure from crest structure pool is received. There is also a folder where rotamers file and other files are stored.
  
As Crest uses very cheap calculations, the energy is not fully reliable. After running crest you should go through the conformer list, pick the conformation which differ substantially (preferably ~10 structures) and run them with more precise calculation (for example #B97/SDD opt in Gaussian). Based on the outcome of this second calculation you should decide which structures you want to submit for expensive calculations, frequencies jobs and similar.
+
As Crest uses very cheap calculations, the energies are not fully reliable. After running crest you should go through the conformers list, pick the conformations which differ substantially (preferably ~10 structures) and run them with a more precise calculation (for example #B97/SDD opt in Gaussian). Based on the outcome of this second calculation batch you should decide which structures you want to submit for expensive calculations, frequencies jobs and similar.
  
 
==Disclaimer==
 
==Disclaimer==
Crest is a metadynamics tool which is very useful for generating low-energy structure candidates. The crest-best does not have to be the best structure, but the set of structures (crest-conformers) usually has the best available conformers within. Crest is a powerful and very useful tool, but it should not be a substitute for your brain. Keep attention to the correct definition of charge and spin. If you think there is a way to improve this guide please contact me (Jan).
+
Crest is a metadynamics tool which is very useful for generating low-energy structure candidates. The crest-best does not have to be the best structure, but the set of structures (crest-conformers) usually has the best available conformers within. Crest is a powerful and very useful tool, but it should not be used uncritically. Keep attention to the correct definition of charge and spin. If you think there is a way to improve this guide, please contact me (Jan).
  
 
Happy computing! ;)
 
Happy computing! ;)
 
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Latest revision as of 14:18, 24 June 2022

Prerequisities

General topics

General topics like queue handling, queues and similar are covered in the gaussian wiki entry.

Submitting jobs

Basic syntax of crest submission script is following:

cnorris@lilo7:~$ Crest structure.xyz

where structure.xyz is the structure which you want to submit.

More advanced syntax looks like this:

cnorris@lilo7:~$ Crest structure.xyz -chrg 1 -uhf 0 -quick

Here I've added quick keyword which makes the screening less in-depth but it goes much quicker. I also added chrg keyword to define charge and uhf keyword to define spin state. For more detailed description and full list of keywords, please refer to crest command line arguments documentation.

Processing calculations

Once calculation is finished, conformers list and best structure from crest structure pool is received. There is also a folder where rotamers file and other files are stored.

As Crest uses very cheap calculations, the energies are not fully reliable. After running crest you should go through the conformers list, pick the conformations which differ substantially (preferably ~10 structures) and run them with a more precise calculation (for example #B97/SDD opt in Gaussian). Based on the outcome of this second calculation batch you should decide which structures you want to submit for expensive calculations, frequencies jobs and similar.

Disclaimer

Crest is a metadynamics tool which is very useful for generating low-energy structure candidates. The crest-best does not have to be the best structure, but the set of structures (crest-conformers) usually has the best available conformers within. Crest is a powerful and very useful tool, but it should not be used uncritically. Keep attention to the correct definition of charge and spin. If you think there is a way to improve this guide, please contact me (Jan).

Happy computing! ;)