Macs in Chemistry

Insanely Great Science

Easy Markdown Updated


I use markdown extensively on my websites and I try to keep a track of Markdown editors that are available. I noticed that Easy Markdown has just been updated, according to the release notes the update provides Improved opening of files encoded in various formats and a Bug fix.


ScienceCloud mobile apps released

ScienceCloud is a secure, SaaS-based, mobile-enabled information management and collaboration environment that improves data and knowledge sharing for globally networked researchers. Bi-directional integration between ScienceCloud and existing on-premises systems lets life sciences organizations migrate to the cloud in a measured fashion, continuing to leverage critical legacy applications as long as needed.

Two mobile apps are now available ScienceCloud Projects and ScienceCloud Tasks.


There are many more mobile science apps here


Amber 14 and Amber 14 Tools released


Version 14 of the Amber software suite has been released (There was no "unlucky" Amber13.)

  • Force fields: Amber has two new fixed-charge protein force fields, ff14SB and ff14ipq, a new modular lipid force field, Lipid14, and updates to nucleic acid and carbohydrate force fields.
  • Improved options for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
  • A completely reorganized Reference Manual
  • QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available
  • More features from sander have been added to pmemd for both CPU and GPU platforms, including performance improvements, and support for extra points, multi-dimension replica exchange, a Monte Carlo barostat, ScaledMD, Jarzynski sampling, explicit solvent constant pH, GBSA, and hydrogen mass repartitioning. Support is also included for the latest Kepler, Titan and GTX7xx GPUs.
  • Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations, and a new absolute free energy method.
  • New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.

Amber Tools have also been updated.

Among the new features in AmberTools14:

  • The sander module, our workhorse simulation program, is now a part of AmberTools;
  • Greatly expanded and improved cpptraj program for analyzing trajectories;
  • new documentation and tools for inspecting and modifying Amber parameter files;
  • Improved workflow for setting up and analyzing simulations;
  • new capability for semi-empirical Born-Oppenheimer molecular dynamics;
  • EMIL: a new absolute free energy method using TI;
  • New Free Energy Workflow (FEW) tool automates free energy calculations (LIE, TI, and MM/PBSA-type calculations);
  • Completely reorganized Reference Manual

Python, Chemistry and a Mac 1


After I posted the page on setting up a Mac for Cheminformatics I was asked if I could do something similar for writing chemistry (or Science in general) Python scripts on a Mac. So I’ve written a “How to” page on setting up your Mac to use the iPython notebook and write simple scripts that use Pybel to access OpenBabel.

The page is here Python, Chemistry and a Mac 1, and I’ll probably add more pages/scripts in the future.


Porting of BUDE (Bristol University Docking Engine) to OpenCL.


A recently publication “High Performance in silico Virtual Drug Screening on Many-Core Processors” DOI describes porting BUDE (Bristol University Docking Engine) to OpenCL.

Our highly optimized OpenCL implementation of BUDE sustains 1.43 TFLOP/s on a single NVIDIA GTX 680 GPU, or 46% of peak performance. BUDE also exploits OpenCL to deliver effective performance portability across a broad spectrum of different computer architectures from different vendors, includ- ing GPUs from NVIDIA and AMD, Intel’s Xeon Phi and multi-core CPUs with SIMD instruction sets.

BUDE is now one the fastest HPC applications ever developed and nicely demonstrates the portability of OpenCL across different architectures.

There is a list of GPU accelerated applications here.