Macs in Chemistry

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MOE updated

 

Chemical Computing Group have announced and update to MOE. The MOE 2016.0802 update contains a number of updates to the biomolecule modelling including improved hydrogen bond detection, and addition of a number of unnatural amino acids.

There have also been improvements to MOE/Web MOE/web. The MOE/web version compatibility check has been broadened. MOE/web license waiting has been improved. HTTPS authentication proxy server support has been improved.


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Apple WWDC 2017

 

Apple have announced the date and venue for the 2017 World Wide Developers Conference. WWDC will take place June 5-9, 2017 at the McEnery Convention Center in San Jose, California, USA.

wwwdc17

Registration opens Monday, March 27 at 10:00 a.m. PDT. The opportunity to buy tickets to WWDC17 will be offered by random selection. To register, you must be a member of the Apple Developer Program or Apple Developer Enterprise Program. Tickets sell out very quickly so put an alert in your calendar now.


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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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Tinker Updated

 

The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, and the AMOEBA (2004, 2009, 2013) polarizable atomic multipole force field.

The TINKER package contains a variety of interesting algorithms such as: flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, various continuum solvation treatments including several generalized Born (GB/SA) models, generalized Kirkwood implicit solvation for AMOEBA, an interface to APBS for Poisson-Boltzmann calculations, efficient truncated Newton (TNCG) local optimization, surface areas and volumes with derivatives, free energy calculations via the Bennett Acceptance Ratio (BAR) method, normal mode vibrational analysis, minimization in Cartesian, torsional or rigid body space, symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise neighbor lists and splined spherical energy cutoff methods, particle mesh Ewald (PME) summation for partial charges and polarizable multipoles, a novel reaction field treatment of long range electrostatics, fast distance geometry metrization with better sampling than standard methods, Elber's reaction path algorithm, potential smoothing and search (PSS) methods for global optimization, Monte Carlo Minimization (MCM) for efficient potential surface scanning, tools for fitting charge, multipole and polarization models to QM-based electrostatic potentials and more....

TINKER 8 is a major new release of the Ponder Lab tool set for molecular mechanics and dynamics calculations. An important change in this new version is the switch from old-style common blocks to Fortran modules. Use of modules and greatly increased use of dynamic memory allocation means TINKER can now support very large molecular systems. TINKER 8 also implements improved OpenMP parallelization throughout many parts of the code. Additional big improvements include parallel neighbor list building and updating, and big reduction in iteration needed to converge AMOEBA polarization via an efficient PCG solver. Other changes from the previous TINKER version include new and updated force field parameter sets and numerous minor additions and bug fixes, many of them suggested by users of the package. Please note that as with prior new releases, version 8 is neither backward nor forward compatible with earlier versions of TINKER. In particular, older versions of parameter files should not be used with TINKER 8 executables and vice versa.


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Learning MacroMols VR

 

Learning MacroMols VR is a mobile app where you can experience macromolecules such as DNA, RNA, carbohydrates and protein structures (from the PDB – Protein Data Bank) in a virtual reality, using Google Cardboards.

It allows the viewer to explore DNA, RNA, Carbohydrates and Proteins.

EduChem VR (http://educhem-vr.com), create immersive virtual reality world of atoms and molecules, while playing. All molecules are 3D objects and one very efficient way to learn more and deeper about atoms and bonds is by VR.


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