Macs in Chemistry

Insanely Great Science

Molecular dynamics

SilcsBio Software

 

A recent publication "Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization" DOI caught my eye. Predicting ligand binding affinities is a very challenging process and whilst free energy perturbation methods have proved useful they are very computationally demanding. SILCS looks to give similar accuracy but with reduced computational demands.

The software is available from SILCSBIO and whilst it requires significant compute resources or access to a virtual cluster using Amazon Web Services, the SilcsBio Graphical User Interface (GUI) enables running SILCS and SSFEP simulations and analysing results through a GUI instead of the command line and is available for Mac OSX and Windows. Visualisation of results uses VMD or PYMOL plugins.

trypsin


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Samson tutorials

 

I've been keeping an eye on Samson for a while now and whilst we still wait for the version 1 release the current version sports some interesting developments.

SAMSON is the quickly growing platform for molecular modeling. SAMSON's goal is to make it faster for everyone to design drugs, materials and nanosystems.

There are an increasing number of Elements

SAMSON Elements are modules for SAMSON that you add from SAMSON Connect. The first time you start SAMSON, some default SAMSON Elements are automatically installed

And the documentation now includes some tutorials, the GROMACS Wizard Light help you to easily run GROMACS simulations and get results as plots and simulation trajectories.

As I've mentioned before the Samson scripting API allows you to control Samson using Python.


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AmberTools19 is now available

The latest update to AmberTools is now available.

AmberTools consists of several independently developed packages that work well by themselves, and with Amber18 itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

AmberTools19 (released on April 25, 2019) consists of the following major codes:

  • NAB/sff: a program build molecules, run MD or apply distance geometry restraints using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models
  • antechamber and MCPB: programs to create force fields for general organic molecules and metal centers
  • tleap and parmed: basic preparatory tools for Amber simulations
  • sqm: semiempirical and DFTB quantum chemistry program
  • pbsa: performs numerical solutions to Poisson-Boltzmann models
  • 3D-RISM: solves integral equation models for solvation
  • sander: workhorse program for molecular dynamics simulations
  • mdgx: a program for pushing the boundaries of Amber MD, primarily through parameter fitting. Also includes customizable virtual sites and explicit solvent MD capabilities.
  • cpptraj and pytraj: tools for analyzing structure and dynamics in trajectories
  • MMPBSA.py and amberlite: energy-based analyses of MD trajectories


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The official release of GROMACS 2016.6 is available

 

This release fixes remaining issues found since version 2016.5. All users of the 2016 series are encouraged to update to 2016.6. Please see the link to the release notes below for more details.

You can find the code, documentation, release notes, and test suite at the links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2016.6.tar.gz
Documentation: http://manual.gromacs.org/documentation/2016.6/index.html (including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2016.6.tar.gz


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PLUMED Version 2.5 (Dec 19, 2018)

 

PLUMED is a plugin that works with a large number of molecular dynamics codes. It can be used to analyze features of the dynamics on-the-fly or to perform a wide variety of free energy methods. PLUMED can also work as a Command Line Tools to perform analysis on trajectories saved in most of the existing formats.

Huge number of changes.

PLUMED: A portable plugin for free-energy calculations with molecular dynamics DOI


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TTClust : A molecular simulation clustering program

 

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):

sudo activate-global-python-argcomplete

Pasted Graphic


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Schrödinger Software Release 2018-2

 

Schrödinger have announced a major update their software suite.

Full details are here https://www.schrodinger.com/newfeatures


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Google Sumer of code, Open Chemistry Projects

 

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!!


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Amber 18 and AmberTools 18released

 

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


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GROMACS 2016.4 has been released

 

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

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Gromacs updated

 

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.


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