Macs in Chemistry

Insanely Great Science

GROMACS updated

 

The official release of GROMACS 2018 is now available.

GROMACS is one of the major software packages for the simulation of biological macromolecules.

Highlights from this update include:-

  • PME long-ranged interactions can now run on a single GPU, which means many fewer CPU cores are needed for good performance.
  • Optimized SIMD support for recent CPU architectures: AMD Zen, Intel Skylake-X and Skylake Xeon-SP.

  • The AWH (Accelerated Weight Histogram) method is now supported, which is an adaptive biasing method used for overcoming free energy barriers and calculating free energies (see http://dx.doi.org/10.1063/1.4890371).

  • A new dual-list dynamic-pruning algorithm for the short-ranged interactions, that uses an inner and outer list to permit a longer-lived outer list, while doing less work overall and making runs less sensitive to the choice of the “nslist” parameter.
  • A physical validation suite is added, which runs a series of short simulations, to verify the expected statistical properties, e.g. of energy distributions between the simulations, as a sensitive test that the code correctly samples the expected ensemble.
  • Conserved quantities are computed and reported for more integration schemes - now including all Berendsen and Parrinello-Rahman schemes.

Comments

Fortran on a Mac

 

I was sent a few updates over the Christmas break and so I've updated the Fortran on a Mac page.


Comments

SeeSAR for Parallelized Fragment Growing & Pocket Exploration

 

I see that SeeSAR now supports a parallelized 'real' fragment growing.

SeeSAR is a software tool for interactive, visual compound prioritisation as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximise the likelihood of success, rather than affinity alone. Having the relevant parameters at hand in combination with real-time visual computer assistance in 3D is one of the strengths of SeeSAR. Stimulating exploration with SeeSAR, we have embarked on pursuing a new cheminformatics compute paradigm of "Propose & Validate".

d0029fff-17c1-46ea-8d52-6f925b77101d-medium

You can download SeeSAR here and use it for free for 7 days.

Comments

Behind the Scenes in Real-Life Software Design By Stephen_Wolfram · 48 videos

 

I just stumbled across a fascinating series of lectures. These are recordings of the live discussions behind the ongoing software development led by Stephen Wolfram.

Of particular interest might be the discussion on incorporating chemistry into the Wolfram language.

https://www.twitch.tv/videos/181269427?collection=F82InZg17BQFzw.


Comments

UCSF ChimeraX

 

A recent publication DOI describes an update to the popular molecule viewer UCSF Chimera

UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution.

The application can be downloaded here http://www.rbvi.ucsf.edu/chimerax/download.html

It is important to note that ChimeraX is not backward compatible with Chimera and does not read Chimera session files. It has been tested on MacOS X 10.12. The ChimeraX user interface is implemented in Qt, offering a native-like look and feel on each platform. ChimeraX is largely implemented using Python, an interpreted programming language. To manipulate these very large datasets interactively, ChimeraX uses memory-efficient data structures combined with high-performance algorithms implemented in C++. MacroMolecular Crystallographic Interchange Format (mmCIF) is the preferred format for atomic data in ChimeraX, mmCIF replaces the aged and more limited PDB format and offers a number of advantages.

sym


Comments

Python support in Excel

 

The most popular suggestion on the "How can we improve Excel for Windows" forum is Python as an Excel scripting language with over 4500 votes and it has elicited a comment from the MSFT excel team.

Thanks for the continued passion around this topic. We’d like to gather more information to help us better understand the needs around Excel and Python integration.

Followed by a survey.

Of course one would hope that they also add it to the Mac version of Excel.

Comments

Suggestions for a Laser Pointer

 

I give a course that consists of a full day of lectures, in the past I've had to use a selection of laser pointers/batteries because they don't last.

So I'm looking for a laser pointer that will last for several hours, and be bright enough to show up on the large flat screens used in many lecture theatres these days.

Any suggestions welcome.


Comments

Predicting the Conformational Energy of Small Molecules

 

An interesting publication in JCIM, Atom Types Independent Molecular Mechanics Method for Predicting the Conformational Energy of Small Molecules, DOI.

We report herein our effort to incorporate lone pairs into our model to extend its applicability domain to any saturated small molecules. The developed model H-TEQ 2 has been validated on a wide variety of molecules from polyaromatic molecules to carbohydrates and molecules with high heteroatoms/carbon ratios.


Comments

Deep Learning Cheat Sheet (using Python Libraries)

 

Just came across this really invaluable resource.

  • Deep Learning Cheat Sheet (using Python Libraries)
  • PySpark Cheat Sheet: Spark in Python
  • Data Science in Python: Pandas Cheat Sheet
  • Cheat Sheet: Python Basics For Data Science
  • A Cheat Sheet on Probability
  • Cheat Sheet: Data Visualization with R
  • New Machine Learning Cheat Sheet by Emily Barry
  • Matplotlib Cheat Sheet
  • One-page R: a survival guide to data science with R
  • Cheat Sheet: Data Visualization in Python
  • Stata Cheat Sheet
  • Common Probability Distributions: The Data Scientist’s Crib Sheet
  • Data Science Cheat Sheet
  • 24 Data Science, R, Python, Excel, and Machine Learning Cheat Sheets
  • 14 Great Machine Learning, Data Science, R , DataViz Cheat Sheets



Comments

YANK

 

YANK is a GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations.

Features

  • Modular Python framework to facilitate development and testing of new algorithms
  • GPU-accelerated via the OpenMM toolkit
  • Alchemical free energy calculations in both explicit and implicit solvent
  • Hamiltonian exchange among alchemical intermediates with Gibbs sampling framework
  • General Markov chain Monte Carlo framework for exploring enhanced sampling methods
  • Built-in equilibration detection and convergence diagnostics
  • Support for AMBER prmtop/inpcrd files
  • Support for absolute binding free energy calculations
  • Support for transfer free energies (such as hydration or partition free energies)

Install using conda

$ conda config --add channels omnia --add channels conda-forge
$ conda install yank

conda will install dependencies from binary packages automatically, including difficult-to-install packages such as OpenMM, numpy, and scipy. YANK runs on Python 3.5, and Python 3.6


Comments

Mac in Chemistry Annual website review

 

At the end of each year I have a look at the website analytics to see which items were the most popular.

Over the year there were 60,000 unique visitors with 25% visiting the site on multiple occasions. The US provided 30% of the visitors and the UK 10% with Germany, Canada and Japan around 5%. As might be expected 60% of the visitors were using a Mac, but 25% of the visitors were Windows users and 10% iOS. Looking at the last month's Mac visitors, 53% were using Mac OS X 10.13, 25% 10.12 and 12% 10.11.

Safari and Chrome (each 41%) were the most used web browsers with the once dominant Internet Explorer down at 2%.

The most viewed blog pages in 2017 were

The most popular web pages were (other than the main page)

The continued popularity of the Fortran on a Mac web page is interesting, I'm not a big Fortran user but if anyone knows of items that could be added to the page I'd be delighted to hear about them. I've done a couple of updates to the Cheminformatics on a Mac page and I think I'll need to add a section on Bioconda in the future.

Interestingly the Scientific Applications under High Sierra page was of only transient popularity. It seem this update to Mac OSX was relatively benign with very few issues.

2017 also saw the 2000th download of iBabel, iBabel is a GUI (graphical user interface) for the open source cheminformatics toolkit OpenBabel. It also provides an interface to a variety of tools built using OpenBabel and a molecule viewer. I'm planning to do an update to iBabel to take advantage of some of the updates to OpenBabel but if you have any suggestions I'd happy to see if I can include them.

3dviewers

2017 also saw the migration of the website from http to https, a change that went pretty seamlessly with only a couple of minor glitches.

The Twitter feed is increasing in popularity with 390 followers. The most popular tweets were

Creating a Bioconda recipe
RSC meeting on AI in Chemistry

The RSS feed still has around 100 followers

Comments