TTclust DOI is a python program used to cluster molecular dynamics simulation trajectories. It only requires a trajectory and a topology file (compatible with most molecular dynamic packages such as Amber, Gromacs, Chramm, Namd or trajectory in PDB format thanks to the MDtraj package).
It is available on GitHub https://github.com/tubiana/TTClust.
For Mac user
If you have issues with pip, first try to add to pip the --ignore-installed argument : sudo pip install --ignore-installed -r requirements.txt If it still doesn't work, it's maybe because of the System Integrity Protection (SIP). I suggest you in this case install ANACONDA or MINICONDA and restart your terminal afterwards. Normally, the pip command should work because your default python will be the anaconda (or miniconda) python.
If you have still issues with the GUI or missing packages : install with pip :
pip install wxpython==4.0.0b1 pip install pandas pip install ttclust
To activate autocompletion for the argpase module, you have to use this command (only once):
The details of some of the projects taking part in the Google Summer of Code are now online here https://summerofcode.withgoogle.com/organizations/6513013473935360/ under the Open Chemistry header.
Really interesting work includes 3-D coordinate generation, standardising fingerprint APIs, a framework for molecular validation, and standardization and molecular dynamics in Avogadro.
Good luck to all that are taking part!!
Amber is a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active develpment community
Amber 18 ajor new features include:
- Free energy calculations on GPUs
- GPU support for 12-6-4 ion potentials
- Domain decomposition for CPU-parallelism
- Nudged elastic band calculations for pmemd (CPU and partial GPU implementation)
- Constant redox potential calculations, to supplement constant pH simulations
- Support and significant performance improvements for the latest Maxwell, Pascal and Volta GPUs from NVIDIA.
- New pmemd.gem code for advanced force fields, including AMOEB
AmberTools 18 new features include
- CUDA-enabled pbsa solver; extensions for membrane modeling with PB *lambda-dynamics method for constant pH simulations *packmol_memgen tool for building lipids and bilayers *New ("middle") integration algorithms in sander *Build tools based on CMake *Continued updates and extensions to cpptraj: *ability to obtain energies from snapshots of PME simulations *Pairlist and other speedups *improved scripting abilities
Instructions for installing Amber under Mac OSX are here http://ambermd.org/Installation.php
You will need to install gfortran, whilst you can download the binary it might be worth considering using Homebrew as described here
Molecular dynamics simulation in general, and GROMACS in particular, has made it possible to study large and complex biomolecular systems such as membranes and membrane proteins and probe atomic detail that is not accessible to any experimental methods. GROMACS can already use thousands of cores and hundreds of accelerators efficiently in parallel, even for a single quite small system. When adding ensemble-level parallelization with Copernicus the total problem scaling extends another two orders of magnitude.
These release notes document the changes that have taken place in GROMACS since version 2016.3 to fix known issues. It also incorporates all fixes made in version 5.1.4 and several since.
- Fixes where mdrun could behave incorrectly
- Disabled PME tuning with the group scheme
- Fixed value of Ewald shift
- Fixed orientation restraint reference
- Fixed bugs with setup for orientation restraints
- Worked around missing OpenMP implementation in orientation restraints
- Enable group-scheme SIMD kernels on recent AVX extensions
- Fix FEP state with rerun
- Fixed COM pull force with SD
- Fix PBC bugs in the swap code
- Fixed flat-bottomed position restraints with multiple ranks
- Fixed null pointer print in DD
- Improved the “files not present” error message
- Fixed LJ-PME + switch grompp error
- Fixed unused SIMD PME table kernel
- Fixed bugs in most double-precision Simd4 implementations
- Avoid inf in SIMD double sqrt()
- Fix NVML error messages
- Fixed IMD interface malfunctions
- Fixed initial temperature reporting
- Fix exception in SIMD LJ PME solve
- Fixes for gmx tools
- Fixed memory access issues in gmx solvate
- Fixed a consistency check in gmx make_edi for flooding
- Supported quiet trajectory-handling I/O
- Improved documentation
- Migrated much content from the wiki to the user guide
- Corrected the PDF manual to reflect that all tools are called gmx
- Clarified gmx editconf help text
- Added missing .mdp file documentation for the enforced rotation module
- Fixed parameter description for dihedral_restraints
- Replaced instance of “group” by “coord” in pull .mdp documentation
- Portability enhancements
- Supported CUDA 9/Volta for nonbonded kernels
- Really enabled AVX512 in the GROMACS-managed build of FFTW
- Fixed aspects for compiling and running on Solaris
- Fixed AVX512F compiler flags
- Fixed compiler flags for using MKL
- Fixes compilation issues with ARM SIMD
GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available,and can run on central processing units (CPUs) and graphics processing units (GPUs). It is free, open-source software.
These release notes document the changes that have taken place in GROMACS since the initial version 2016 and subsequent patch releases, to fix known issues. It also incorporates all fixes made in version 5.1.4 and several since.
The documentation gives details of installation.