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- AMBER
- Adding a model for PATHSAMPLE
- Adding a model to GMIN
- Adding a model to OPTIM
- Adding example input for Wales group programs
- Adding partially finished OPTIM stationary points to a PATHSAMPLE database
- Advanced colouring
- AlaviGroup
- Anthony & Alston
- Assets
- Aux2bib
- Backup strategy
- Basic linux commands everyone should know!
- BookList
- Bug hunting tips for group code
- CHARMM
- CPMD
- CPMDInput
- Calculating rate constants (GT and fastest path)
- Calculating rate constants (SGT, DGT, and SDGT)
- CamCASP
- CamCASP/BasisSets
- CamCASP/Bugs
- CamCASP/Bugs/1
- CamCASP/Bugs/2
- CamCASP/Bugs/3
- CamCASP/Bugs/4
- CamCASP/Bugs/5
- CamCASP/Bugs/6
- CamCASP/Bugs/7
- CamCASP/Bugs/8
- CamCASP/Bugs/9
- CamCASP/Bugs/9/pyr2-double-Hbonded.clt
- CamCASP/CodeExamples/DirectAccess
- CamCASP/Compilation
- CamCASP/Interfaces
- CamCASP/Notes
- CamCASP/Notes/1
- CamCASP/Notes/2
- CamCASP/Notes/3
- CamCASP/Notes/4
- CamCASP/Notes/5
- CamCASP/Notes/6
- CamCASP/Notes/7
- CamCASP/Notes/8
- CamCASP/Numerical
- CamCASP/PFIT
- CamCASP/Programming
- CamCASP/Programming/0
- CamCASP/Programming/1
- CamCASP/Programming/2
- CamCASP/Programming/3
- CamCASP/Programming/4
- CamCASP/Programming/5
- CamCASP/Programming/5/example1
- CamCASP/Programming/6
- CamCASP/Programming/7
- CamCASP/Programming/8
- CamCASP/Programming/9
- CamCASP/Releases
- CamCASP/ToDo
- CamCASP/ToDo/Memory
- CamCASP/ToDo/diskIO
- CamCasp
- Catherine Pitt
- Chris's 'all you can eat' tips
- Chris Whittleston
- Colourdiscon.py
- Compiling AMBER Tools so you can start making input and analyzing output
- Compiling AMBER Tools so you can start making input and analyzing output!
- Compiling GMIN with CHARMM
- Computer Office services
- Conventions when using LaTex
- Conversion between different data file formats
- Conversion between different image file formats
- Converting between '.crd' and '.pdb'
- Coulomb Integral
- Creating movies (.mpg) of paths using OPTIM
- Dalton
- Data manipulation using 'awk'
- Data manipulation using 'sed'
- David's .inputrc file
- Debugging odd transition states in OPTIM
- Differences from Clust
- DisconnectionDPS
- Doxygen
- EffectiveSupercell
- ElaborateDiff
- Electronic Structure Group Meetings
- Enviroment modules
- Environment modules
- Evaluating different components of AMBER energy function with SANDER
- Extractedmin2pdb.py
- File server options
- Finding an initial path between two end points (minima)
- Finding bugs in latex documents that will not compile
- Fixing thunderbird links
- Fortran conventions for group software
- Fortran issues
- GMIN
- GPU processing
- General queueing problems
- Generating parameters using AMBER's built in General Forcefield (gaff)
- Generating parameters using RESP charges from GAMESS-US
- Getting GMIN from the SVN repository
- Git
- Git-NECI
- Global optimization of biomolecules using AMBER9
- Global optimization of biomolecules using AMBER9 with Structural Restraints
- Gnuplot
- GraphTypes
- GroupPages
- Group wish list
- Here
- IT Equipment wishlist
- Identifying job on a node
- If things go wrong...
- If things go wrong... (perish the thought!)
- If you lost file min.data, but still you have points.min
- If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)
- Installing python modules
- Intel Trace Analyzer and Collector
- James Spencer
- Known Bugs
- LDAP plans
- Lapack compilation
- Latex2html
- LinuxTips
- List of output files for PATHSAMPLE
- Loading coordinate files into VMD with the help of an AMBER topology file
- Main Page
- Makerestart
- Maui compilation
- Mek-quake Queueing system
- Mek-quake initial setup notes
- Minimizing a structure using OPTIM
- Minimizing a structure using OPTIM and AMBER9
- Mounting sharedscratch locally
- NECI
- NECI-testcode
- NECI Parallelization
- NECI Re-write
- New mek-quake
- OPTIM
- OPTIM output files
- OPTIM output files (some of the them at least)
- OS X and Linux tips
- Optimising a path
- Organizing papers with tellico
- Other IT stuff
- Other useful scipts
- Other useful scripts
- PATHSAMPLE
- ParallelCode
- Path.info file is not read, causes PATHSAMPLE to die
- Path2pdb.py
- Path2xyz.py
- Pdb to movie.py
- Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)
- PeriodicImages
- Perm-pdb.py
- Perm-prmtop.py
- Pgi64/8.0/1
- Piping and redirecting output from one command or file to another
- Plotting data in real time
- Preparing an AMBER topology file for a protein plus ligand system
- Preparing an AMBER topology file for a protein system
- Printing files from the command line using 'lpr'
- Producing a PDB from a coordinates and topology file
- Producing sexy ray-traced images
- Programming
- Progress
- Proposed changes to backup and archiving
- Pymol
- Queueing system
- Quick guide to awk
- REMD with AMBER
- REX (Replica EXchange MD) with the MMTSB-toolset
- Rama upgrade
- Recommended bash aliases
- Relaxing existing minima and creating new database
- Relaxing existing minima with new potential and creating new database
- Relaxing existing transition states with new potential and creating new database
- Remastering Knoppix
- Removing an excessive number of files from a directory - when 'rm' just isn't enough
- Removing minima and transition states from the database
- Restarting a GMIN run from a dump file
- Revamping the modules system
- Rotatating integrals
- Running GMIN with MD move steps AMBER
- Running a G\=o model with the AMHGMIN
- Running a Go model with the AMHGMIN
- Running programs in the background
- Runtime diagnostics with ifort
- SVN Page
- SVN Wisdom Page
- SVN setup
- See unpacked nodes
- Selecting search parameters for GMIN
- Setting up aliases to quickly log you in to a different machine
- Short 'awk' examples
- Short 'sed' examples
- Simple scripts for LEaP to create topology and coordinate files
- Some short 'sed' examples
- SuSE 10.1 workstation image
- SuSE 10.2 workstation image
- SuSE 10.3 workstation image
- SuSE 11.1
- Submitting jobs, interactively or to a cluster queue system
- Symmetry
- Tardis scheduling policy
- The effect of calculating less than the maximum number of eigenvalues using ENDHESS n
- To Do
- Torque and Maui
- Transfering files to and from your workstation
- Upgrading destiny
- Upgrading sword
- Useful .vmdrc file
- Useful Makefiles
- Useful PBS scripts
- Useful Python Scripts
- Using 'ssh-keygen' to automatically log you into clusters from your workstation
- Using BHINTERP to find minima between two end points
- Using Molfacture to edit molecules and add hydrogens
- Using VMD to display and manipulate '.pdb' files
- Using tar and gzip to compress/uncompress files
- Using the implicit membrane model IMM1
- VMD
- Version control
- Visitor policy
- Visualising normal modes using VMD and OPTIM
- Wales Group
- Wales Group Conventions when using LaTex
- Wales Group Fortran conventions for group software
- Wales Group Version control
- Wales group calendars
- Xfig
- Xmakemol
- Xmgrace
- Zippo Sicortex machine