Difference between revisions of "Wales Group"
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The official documentation can be found [http://www-wales.ch.cam.ac.uk/software.html here]. It is highly reccomended that before you start any jobs, you check the documentation to make sure you understand what each keyword you have specified does and if it's necessary! The links below provide a few working examples for each program the group uses, from initial setup to job submission. |
The official documentation can be found [http://www-wales.ch.cam.ac.uk/software.html here]. It is highly reccomended that before you start any jobs, you check the documentation to make sure you understand what each keyword you have specified does and if it's necessary! The links below provide a few working examples for each program the group uses, from initial setup to job submission. |
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| + | * [[GMIN]]: A program for finding global minima and calculating thermodynamic properties from basin-sampling. |
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| − | * [[GMIN]] |
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| + | * [[OPTIM]]: A program for optimizing geometries and calculating reaction pathways |
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| − | * [[OPTIM]] |
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| + | * [[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis |
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| − | * [[PATHSAMPLE]] |
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* [[VMD]] |
* [[VMD]] |
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* [[Pymol]] |
* [[Pymol]] |
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| + | |||
| + | == Useful scripts == |
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| + | |||
| + | * [[perm-prmtop.py]]: A python program for preparing a new topology file for Amber9 |
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Revision as of 10:15, 29 April 2008
Members:
- Dr David J. Wales
- Szilard Fejer
- Chris Whittleston
- Hayley McKay
- Dr Joanne Carr
- Dr Dwaipayan Chakrabarti
- Dr Edyta Malolepsza
- Dr Birgit Strodel
This page is intended to be an index of useful info concerning group practice and use of software including tutorials. Please feel free to add any notes you have on software use and especially on common problems you encounter.
Group software
The official documentation can be found here. It is highly reccomended that before you start any jobs, you check the documentation to make sure you understand what each keyword you have specified does and if it's necessary! The links below provide a few working examples for each program the group uses, from initial setup to job submission.
- GMIN: A program for finding global minima and calculating thermodynamic properties from basin-sampling.
- OPTIM: A program for optimizing geometries and calculating reaction pathways
- PATHSAMPLE: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis
Other useful software
Useful scripts
- perm-prmtop.py: A python program for preparing a new topology file for Amber9