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- AMBER
- 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 Wales Group codes 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
- Getting started with SLURM
- Git Workflow
- Global optimization of biomolecules using AMBER9
- Global optimization of biomolecules using AMBER9 with Structural Restraints
- Global optimization of biomolecules using CHARMM
- Gnuplot
- IMPORTANT: Using PATHSAMPLE safely on sinister
- Identifying job on a node
- Identifying the k fastest paths between endpoints using KSHORTESTPATHS
- If things go wrong...
- 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 GROMACS on Clust
- Installing and setting up the MMTSB toolset
- Installing packages on your managed CUC3 workstation
- Installing python modules
- Instanton tunneling and classical rate calculations with OPTIM
- Intel Trace Analyzer and Collector
- Interactive jobs on cluster
- Jenkins CI
- Keywords
- LDAP plans
- Lapack compilation
- Latex2html
- Ligand binding-mode searches with HBONDMATRIX
- Linear and non-linear regression in gnuplot
- List of output files for PATHSAMPLE
- Loading AMBER prmtop and inpcrd files into Pymol
- Loading OPTIM's min.data.info files into PATHSAMPLE
- Loading coordinate files into VMD with the help of an AMBER topology file
- Local Rigid Body Framework
- Local rigid body in OPTIM
- MMTSB-toolset
- Main Page
- Makerestart
- Managing interactive jobs on cluster
- Maui compilation
- Mek-quake Queueing system
- Mek-quake initial setup notes
- Mercurial
- Migrating to the new SVN server
- Minimizing a structure using OPTIM and AMBER9
- Minimizing a structure using OPTIM and CHARMM
- Mounting sharedscratch locally
- Mutational BH steps
- NECI Parallelization
- New mek-quake
- No Frequency Warning
- Notes on AMBER 12 interface
- Notes on MINPERMDIST
- OPTIM
- OPTIM/Q-Chem Tutorial
- OPTIM and PY ellipsoids tutorial
- OPTIM output files
- Optimising a path
- Optimization tricks
- Other IT stuff
- PATHSAMPLE
- PYGMIN & DMACRYS
- Parameter-scanning script
- Path.info file is not read, causes PATHSAMPLE to die
- Path2pdb.py
- Path2xyz.py
- Pathsampling short paths
- Pathsampling short paths (CHARMM)
- Pathway Gap Filling Post-CHECKSPMUTATE
- Pdb to movie.py
- Pele
- Performing a hydrogen-bond analysis
- Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)
- Perm-pdb.py
- Perm-prmtop.py
- Pgprof
- Piping and redirecting output from one command or file to another
- PlotGMINms.tcl
- Plotting a quick histogram in gnuplot using the raw data
- Plotting data in real time
- Porfuncs Documentation
- Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays
- Preparing an AMBER topology file for a protein plus ligand system
- Preparing an AMBER topology file for a protein system
- Preparing input files for a peptide using AMBER
- Printing files from the command line using 'lpr'
- Producing a PDB from a coordinates and topology file
- Producing sexy ray-traced images
- Program flow
- Progress
- Proposed changes to backup and archiving
- Pymol
- Python interface for GMIN/OPTIM
- Quasi-continuous interpolation for biomolecules
- Quick guide to awk
- REMD with AMBER
- REX (Replica EXchange MD) with the MMTSB-toolset
- Rama upgrade
- Recommended bash aliases
- 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
- Rigid body input files for proteins using genrigid-input.py
- Rotamer moves in AMBER
- Running GMIN with MD move steps AMBER
- Running Wales Group software on Windows 7
- Running a G\=o model with the AMHGMIN
- Running a Go model with the AMHGMIN
- Running an Gaussian03 interfaced OPTIM job
- Running programs in the background
- STARTING INITIAL PATH JOBS WITH PATHSAMPLE
- SVN setup
- See unpacked nodes
- Selecting search parameters for GMIN
- Setting up
- Setting up (CHARMM)
- 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
- Simulations using OPEP
- Sorting a file by multiple columns
- 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
- Symmetrising AMBER topology files
- Tardis scheduling policy
- The effect of calculating less than the maximum number of eigenvalues using ENDHESS n
- Thomson problem in OPTIM
- Torque and Maui
- Transfering files to and from your workstation
- Upgrading destiny
- Upgrading sword
- Uploading non image files to the wiki
- Useful .vmdrc file
- Using 'ssh-keygen' to automatically log you into clusters from your workstation
- Using AMBER 14 on the GPU and compute clusters
- Using BHINTERP to find minima between two end points
- Using GMIN and OPTIM with GPUs
- Using GMIN to generate endpoints
- Using GMIN to generate endpoints (CHARMM)
- 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
- VMD script to annotate each frame of a trajectory
- Victor Ruehle
- Visualising normal modes using VMD and OPTIM
- Wales Group
- Wales Group Version control
- When PATHSAMPLE finds a connected path, but using DIJKSTRA 0 fails to find the connected path
- Xfig
- Xmakemol
- Xmgrace
- Zippo Sicortex machine