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- A guide to using SLURM to run GPU jobs on pat
- A guide to using SLURM to run PATHSAMPLE
- Adding a model for PATHSAMPLE
- Adding a model to GMIN
- Adding a model to OPTIM
- Adding partially finished OPTIM stationary points to a PATHSAMPLE database
- Adding several minima obtained using GMIN (maybe using BHPT) to min.data
- Advanced colouring
- Allowing read access to your directories
- Alternatively, making the initial path with PATHSAMPLE itself
- Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)
- Amberinterface
- Angle-axis framework
- Automatic Rigid Body Grouping
- Aux2bib
- BLJ60 example input
- BLJ60 example setup
- Backup strategy
- Bash history searching
- Bash loop tricks
- Basic linux commands everyone should know!
- Beginner's guide to working in Wales group
- Biomolecules in PATHSAMPLE
- Biomolecules in the energy landscape framework
- Blacklisting Compilers
- Branching and Merging
- CAMSHIFT
- CHARMM
- CHECKSPMUTATE
- CPMDInput
- Calculating binding free energy using the FSA method
- Calculating energy of a conformation
- Calculating molecular properties
- Calculating order parameters
- Calculating rate constants (GT and fastest path)
- Calculating rate constants (SGT, DGT, and SDGT)
- CamCASP/Bugs
- CamCASP/CodeExamples/DirectAccess
- CamCASP/Notes
- CamCASP/Programming
- CamCASP/Programming/5/example1
- CamCASP/ToDo/Memory
- CamCASP/ToDo/diskIO
- CamCasp
- Chain crossing
- Cmake interface building
- Colourdiscon.py
- Common setup problem : No Frequency Warning
- Compiler Flags
- Compiling Wales Group code using CMake
- Compiling and using GMIN with QUIP
- Compiling and using OPTIM with QUIP
- Comprehensive Contents Page
- Computer Office services
- Computing CHARMM FF energy using GMIN, MMTSB and CHARMM
- Computing normal modes in angle-axis
- Computing values only once
- Connecting Sub-databases
- Connecting two minima with a pathway
- Constructing Free Energy Disconnectivity Graphs
- Conversion between different data file formats
- Conversion between different image file formats
- Converting between '.crd' and '.pdb'
- Creating mismatched DNA duplex using NAB
- Creating movies (.mpg) of paths using OPTIM
- DISCOTRESS
- DMACRYS interface
- DMAGMIN setup
- David's .inputrc file
- Debugging odd transition states in OPTIM
- Decoding heat capacity curves
- Density of states and thermodynamics from energy distributions at different temperatures
- Differences from Clust
- Dijkstra test.py
- DisconnectionDPS
- ElaborateDiff
- Ellipsoid.model
- Ellipsoid.model.xyz
- Ellipsoid.xyz
- Evaluating different components of AMBER energy function with SANDER
- Expanding the kinetic transition network with PATHSAMPLE
- Expanding the kinetic transition network with PATHSAMPLE (CHARMM)
- Extractedmin2pdb.py
- Finding an initial path between two end points (minima)
- Finding an initial path with OPTIM and starting up PATHSAMPLE
- Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)
- Finding bugs in latex documents that will not compile
- Fine tuning UNTRAP
- Fixing thunderbird links
- GMIN
- GMIN MOVES module
- GMIN SANITY module
- GMIN TESTS module
- GenCoords
- GenCoords Models
- Gencoords
- Generating a GMIN Eclipse project
- Generating parameters using AMBER's built in General Forcefield (gaff)
- Generating parameters using RESP charges from GAMESS-US
- Generating pdb, crd and psf for a peptide sequence