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Showing below up to 250 results in range #1 to #250.
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- Calculating energy of a conformation (1 revision)
- Converting between '.crd' and '.pdb' (1 revision)
- Ellipsoid.xyz (1 revision)
- GenCoords Models (1 revision)
- If you lost file min.data, but still you have points.min (1 revision)
- List of output files for PATHSAMPLE (1 revision)
- PYGMIN & DMACRYS (1 revision)
- PlotGMINms.tcl (1 revision)
- Quasi-continuous interpolation for biomolecules (1 revision)
- Running Wales Group software on Windows 7 (1 revision)
- Sorting a file by multiple columns (1 revision)
- Using 'ssh-keygen' to automatically log you into clusters from your workstation (1 revision)
- When PATHSAMPLE finds a connected path, but using DIJKSTRA 0 fails to find the connected path (1 revision)
- Calculating molecular properties (1 revision)
- Compiler Flags (1 revision)
- Evaluating different components of AMBER energy function with SANDER (1 revision)
- Gencoords (1 revision)
- If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing) (1 revision)
- Loading AMBER prmtop and inpcrd files into Pymol (1 revision)
- Mounting sharedscratch locally (1 revision)
- Parameter-scanning script (1 revision)
- Plotting a quick histogram in gnuplot using the raw data (1 revision)
- Quick guide to awk (1 revision)
- Running a G\=o model with the AMHGMIN (1 revision)
- SuSE 10.1 workstation image (1 revision)
- Using AMBER 14 on the GPU and compute clusters (1 revision)
- A guide to using SLURM to run GPU jobs on pat (1 revision)
- Xfig (1 revision)
- BLJ60 example setup (1 revision)
- Backup strategy (1 revision)
- Calculating order parameters (1 revision)
- Expanding the kinetic transition network with PATHSAMPLE (1 revision)
- Generating a GMIN Eclipse project (1 revision)
- Installing GROMACS on Clust (1 revision)
- Mutational BH steps (1 revision)
- Path.info file is not read, causes PATHSAMPLE to die (1 revision)
- Plotting data in real time (1 revision)
- REMD with AMBER (1 revision)
- Running a Go model with the AMHGMIN (1 revision)
- SuSE 10.2 workstation image (1 revision)
- Using BHINTERP to find minima between two end points (1 revision)
- A guide to using SLURM to run PATHSAMPLE (1 revision)
- Xmakemol (1 revision)
- Xmgrace (1 revision)
- Bash history searching (1 revision)
- Calculating rate constants (GT and fastest path) (1 revision)
- Expanding the kinetic transition network with PATHSAMPLE (CHARMM) (1 revision)
- Generating parameters using AMBER's built in General Forcefield (gaff) (1 revision)
- Installing and setting up the MMTSB toolset (1 revision)
- Loading coordinate files into VMD with the help of an AMBER topology file (1 revision)
- NECI Parallelization (1 revision)
- Path2pdb.py (1 revision)
- Porfuncs Documentation (1 revision)
- REX (Replica EXchange MD) with the MMTSB-toolset (1 revision)
- Running an Gaussian03 interfaced OPTIM job (1 revision)
- SuSE 10.3 workstation image (1 revision)
- Using GMIN and OPTIM with GPUs (1 revision)
- Adding a model for PATHSAMPLE (1 revision)
- Zippo Sicortex machine (1 revision)
- Bash loop tricks (1 revision)
- Calculating rate constants (SGT, DGT, and SDGT) (1 revision)
- Compiling and using GMIN with QUIP (1 revision)
- DMACRYS interface (1 revision)
- Extractedmin2pdb.py (1 revision)
- Generating parameters using RESP charges from GAMESS-US (1 revision)
- Installing packages on your managed CUC3 workstation (1 revision)
- Local Rigid Body Framework (1 revision)
- New mek-quake (1 revision)
- Path2xyz.py (1 revision)
- Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays (1 revision)
- Rama upgrade (1 revision)
- Running programs in the background (1 revision)
- SuSE 11.1 (1 revision)
- Adding a model to GMIN (1 revision)
- Basic linux commands everyone should know! (1 revision)
- CamCASP/Bugs (1 revision)
- Compiling and using OPTIM with QUIP (1 revision)
- DMAGMIN setup (1 revision)
- Generating pdb, crd and psf for a peptide sequence (1 revision)
- Installing python modules (1 revision)
- Local rigid body in OPTIM (1 revision)
- Preparing an AMBER topology file for a protein plus ligand system (1 revision)
- Recommended bash aliases (1 revision)
- Submitting jobs, interactively or to a cluster queue system (1 revision)
- CamCASP/CodeExamples/DirectAccess (1 revision)
- David's .inputrc file (1 revision)
- Instanton tunneling and classical rate calculations with OPTIM (1 revision)
- MMTSB-toolset (1 revision)
- Notes on AMBER 12 interface (1 revision)
- Pathsampling short paths (CHARMM) (1 revision)
- Relaxing existing minima with new potential and creating new database (1 revision)
- Using Molfacture to edit molecules and add hydrogens (1 revision)
- Adding partially finished OPTIM stationary points to a PATHSAMPLE database (1 revision)
- Biomolecules in PATHSAMPLE (1 revision)
- CamCASP/Notes (1 revision)
- Computer Office services (1 revision)
- Debugging odd transition states in OPTIM (1 revision)
- Intel Trace Analyzer and Collector (1 revision)
- Notes on MINPERMDIST (1 revision)
- Relaxing existing transition states with new potential and creating new database (1 revision)
- See unpacked nodes (1 revision)
- Tardis scheduling policy (1 revision)
- Using VMD to display and manipulate '.pdb' files (1 revision)
- Adding several minima obtained using GMIN (maybe using BHPT) to min.data (1 revision)
- Biomolecules in the energy landscape framework (1 revision)
- CamCASP/Programming (1 revision)
- Computing CHARMM FF energy using GMIN, MMTSB and CHARMM (1 revision)
- Finding bugs in latex documents that will not compile (1 revision)
- Global optimization of biomolecules using AMBER9 (1 revision)
- Makerestart (1 revision)
- Pdb to movie.py (1 revision)
- Printing files from the command line using 'lpr' (1 revision)
- Remastering Knoppix (1 revision)
- Selecting search parameters for GMIN (1 revision)
- The effect of calculating less than the maximum number of eigenvalues using ENDHESS n (1 revision)
- Using tar and gzip to compress/uncompress files (1 revision)
- Advanced colouring (1 revision)
- Blacklisting Compilers (1 revision)
- CamCASP/Programming/5/example1 (1 revision)
- Computing normal modes in angle-axis (1 revision)
- Density of states and thermodynamics from energy distributions at different temperatures (1 revision)
- Fine tuning UNTRAP (1 revision)
- Global optimization of biomolecules using AMBER9 with Structural Restraints (1 revision)
- Jenkins CI (1 revision)
- Managing interactive jobs on cluster (1 revision)
- OPTIM/Q-Chem Tutorial (1 revision)
- Pele (1 revision)
- Producing a PDB from a coordinates and topology file (1 revision)
- Removing an excessive number of files from a directory - when 'rm' just isn't enough (1 revision)
- Thomson problem in OPTIM (1 revision)
- Using the implicit membrane model IMM1 (1 revision)
- Allowing read access to your directories (1 revision)
- Branching and Merging (1 revision)
- CamCASP/ToDo/Memory (1 revision)
- Computing values only once (1 revision)
- Differences from Clust (1 revision)
- Fixing thunderbird links (1 revision)
- Global optimization of biomolecules using CHARMM (1 revision)
- Keywords (1 revision)
- Maui compilation (1 revision)
- OPTIM and PY ellipsoids tutorial (1 revision)
- Performing a hydrogen-bond analysis (1 revision)
- Producing sexy ray-traced images (1 revision)
- Removing minima and transition states from the database (1 revision)
- Torque and Maui (1 revision)
- CAMSHIFT (1 revision)
- CamCASP/ToDo/diskIO (1 revision)
- Dijkstra test.py (1 revision)
- Gnuplot (1 revision)
- LDAP plans (1 revision)
- Mek-quake Queueing system (1 revision)
- Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM) (1 revision)
- Program flow (1 revision)
- Restarting a GMIN run from a dump file (1 revision)
- Setting up aliases to quickly log you in to a different machine (1 revision)
- Transfering files to and from your workstation (1 revision)
- VMD script to annotate each frame of a trajectory (1 revision)
- CHARMM (1 revision)
- CamCasp (1 revision)
- GMIN MOVES module (1 revision)
- IMPORTANT: Using PATHSAMPLE safely on sinister (1 revision)
- Lapack compilation (1 revision)
- Mek-quake initial setup notes (1 revision)
- Perm-pdb.py (1 revision)
- Progress (1 revision)
- Revamping the modules system (1 revision)
- Short 'awk' examples (1 revision)
- Upgrading destiny (1 revision)
- Victor Ruehle (1 revision)
- Amberinterface (1 revision)
- Chain crossing (1 revision)
- Constructing Free Energy Disconnectivity Graphs (1 revision)
- ElaborateDiff (1 revision)
- GMIN SANITY module (1 revision)
- Identifying job on a node (1 revision)
- Latex2html (1 revision)
- Mercurial (1 revision)
- Optimization tricks (1 revision)
- Perm-prmtop.py (1 revision)
- Proposed changes to backup and archiving (1 revision)
- Rigid body input files for proteins using genrigid-input.py (1 revision)
- Short 'sed' examples (1 revision)
- Upgrading sword (1 revision)
- Visualising normal modes using VMD and OPTIM (1 revision)
- Angle-axis framework (1 revision)
- CPMDInput (1 revision)
- Cmake interface building (1 revision)
- Conversion between different data file formats (1 revision)
- Ellipsoid.model (1 revision)
- GMIN TESTS module (1 revision)
- Identifying the k fastest paths between endpoints using KSHORTESTPATHS (1 revision)
- Ligand binding-mode searches with HBONDMATRIX (1 revision)
- Migrating to the new SVN server (1 revision)
- Other IT stuff (1 revision)
- Pgprof (1 revision)
- Pymol (1 revision)
- Rotamer moves in AMBER (1 revision)
- Simple scripts for LEaP to create topology and coordinate files (1 revision)
- Uploading non image files to the wiki (1 revision)
- Automatic Rigid Body Grouping (1 revision)
- Calculating binding free energy using the FSA method (1 revision)
- Colourdiscon.py (1 revision)
- Conversion between different image file formats (1 revision)
- Ellipsoid.model.xyz (1 revision)
- GenCoords (1 revision)
- If things go wrong... (1 revision)
- Linear and non-linear regression in gnuplot (1 revision)
- Piping and redirecting output from one command or file to another (1 revision)
- Python interface for GMIN/OPTIM (1 revision)
- Running GMIN with MD move steps AMBER (1 revision)
- Simulations using OPEP (1 revision)
- Useful .vmdrc file (1 revision)
- Aux2bib (1 revision)
- Finding an initial path between two end points (minima) (2 revisions)
- No Frequency Warning (2 revisions)
- STARTING INITIAL PATH JOBS WITH PATHSAMPLE (2 revisions)
- Preparing an AMBER topology file for a protein system (2 revisions)
- Symmetrising AMBER topology files (2 revisions)
- Decoding heat capacity curves (2 revisions)
- OPTIM output files (2 revisions)
- Minimizing a structure using OPTIM and AMBER9 (2 revisions)
- Common setup problem : No Frequency Warning (3 revisions)
- Minimizing a structure using OPTIM and CHARMM (3 revisions)
- AMBER (3 revisions)
- BLJ60 example input (3 revisions)
- DISCOTRESS (3 revisions)
- Getting started with SLURM (3 revisions)
- OPTIM (3 revisions)
- Alternatively, making the initial path with PATHSAMPLE itself (3 revisions)
- Connecting two minima with a pathway (3 revisions)
- Optimising a path (3 revisions)
- Using GMIN to generate endpoints (4 revisions)
- Adding a model to OPTIM (4 revisions)
- Finding an initial path with OPTIM and starting up PATHSAMPLE (4 revisions)
- SVN setup (4 revisions)
- Interactive jobs on cluster (4 revisions)
- Setting up (4 revisions)
- VMD (4 revisions)
- Wales Group (4 revisions)
- Pathsampling short paths (5 revisions)
- Wales Group Version control (5 revisions)
- Alternatively, making the initial path with PATHSAMPLE itself (CHARMM) (6 revisions)
- Compiling Wales Group code using CMake (7 revisions)
- Beginner's guide to working in Wales group (8 revisions)
- Creating movies (.mpg) of paths using OPTIM (10 revisions)
- Compiling Wales Group codes using cmake (10 revisions)
- Using GMIN to generate endpoints (CHARMM) (11 revisions)
- DisconnectionDPS (11 revisions)
- PATHSAMPLE (12 revisions)
- Loading OPTIM's min.data.info files into PATHSAMPLE (13 revisions)