Software

 

CLASSICAL MOLECULAR DYNAMICS


GROMACS

GROMACS is the premier statistical mechanics tool that is freely available to the scientific community. 

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition:

  • GROMACS provides extremely high performance compared to all other programs. A lot of algorithmic optimizations have been introduced in the code; we have for instance extracted the calculation of the virial from the innermost loops over pairwise interactions, and we use our own software routines to calculate the inverse square root. The innermost loops are generated automatically in either C or Fortran at compile time, with optimizations adopted to your architecture. Assembly loops using SSE and 3DNow! multimedia instructions are provided for i386 processors, separate versions using all x86-64 registers are used on Opteron x86-64 and Xeon EM64t machines. 
     
  • GROMACS is user-friendly, with topologies and parameter files written in clear text format. There is a lot of consistency checking, and clear error messages are issued when something is wrong. Since the C preprocessor is used, you can have conditional parts in your topologies and include other files. You can even compress most files and GROMACS will automatically pipe them through gzip upon reading.
     
  • There is no scripting language - all programs use a simple interface with command line options for input and output files. You can always get help on the options by using the -h option, or use the extensive manuals provided free of charge in electronic or paper format. There is also an integrated graphical user interface available for all programs.
     
  • As the simulation is proceeding, GROMACS will continuously tell you how far it has come, and what time and date it expects to be finished.
     
  • Both run input files and trajectories are independent of hardware endian and can thus be read by any version GROMACS, even if it was compiled using a different floating-point precision. All files from GROMACS 2.0 can further be used in the new version 3!
     
  • GROMACS can write coordinates using lossy compression, which provides a very compact way of storing trajectory data. The accuracy can be selected by the user.
     
  • GROMACS comes with a large selection of flexible tools for trajectory analysis - you won't have to write any code to perform routine analyses. The output is further provided in the form of finished Xmgr/Grace graphs, with axis labels, legends, etc. already in place!
     
  • A basic trajectory viewer that only requires standard X libraries is included, and several external visualization tools can read the GROMACS file formats.
     
  • GROMACS can be run in parallel, using standard MPI communication.
     
  • GROMACS contains several state-of-the-art algorithms that make it possible to extend the time steps is simulations significantly, and thereby further enhance performance without sacrificing accuracy or detail.
     
  • The package includes a fully automated topology builder for proteins, even multimeric structures. Building blocks are available for the 20 standard amino acid residues as well as some modified ones, the 4 nucleotide and 4 deoxinucleotide residues, several sugars and lipids, and some special groups like hemes and several small molecules.
     
  • There is ongoing development to extend GROMACS with interfaces both to Quantum Chemistry and Bioinformatics/databases.
     
  • GROMACS is Free Software, available under the GNU General Public License.
     
  • GROMACS is my tool of choice for performing Newtonian Molecular Dynamics simulations

TINKER

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 AMBER94/96, CHARMM27, MM2(1991), MM3(2000), OPLS-AA and OPLS-UA.

My primary use for TINKER is Molecular Dynamics and the analysis of results from these simulations.. The organization and documentation of the TINKER source code are among the best I have ever seen. The source code and associated executables are available free of charge and are downloadable from http://dasher.wustl.edu/tinker/. Jay Ponder and his group provide excellent support for this outstanding package.

QUANTUM CHEMISTRY TOOLS

Firefly

Firefly (previously called PCGAMESS) is my Quantum Chemistry tool of choice. It's free, the people who manage the source code will actually let me work as a part of their team to implement new features, it has most of the methods I need to apply, and it is quite efficient (i.e. fast) in performing the calculations that are of interest to me.

In addition, we incorporated Tinker Molecular Mechanics capabilities into v6.4 of PC-GAMESS (the predecessor of Firefly) so it can do QC/MM hybrid calculations. It can use all the atomistic molecular force fields available in Tinker (MM2. MM3, OPLS, OPLSAA, CHARMM, AMBER) as well as the UFF we integrated into Tinker with Dr. Jay Ponder and his group. We thank Dr. Ponder for his kind permission to use the Tinker code in FireFly.

Firefly is developed and maintained by Alex A. Granovsky.  Its web site is located here

Firefly is a derivative of the GAMESS program developed at Iowa State University by M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.J.Su, T.L.Windus, Together With M.Dupuis, J.A.Montgomery J.Comput.Chem. 14, 1347-1363(1993). Their web site is located here.

ArgusLab

ArgusLab is an excellent program for generating molecular models, doing calculations using semi-empirical and UFF methods, and visualizing the results of QC calculations. I use it primarily for model building and some visualization. It is developed by the people at Planaria Software who can be located here.

ORCA

The program ORCA is a modern electronic structure program package written by F. Neese, with contributions from U. Becker, D. Ganiouchine, S. Koßmann, T. Petrenko, C. Riplinger and F. Wennmohs. The binaries of ORCA are available free of charge for academic users for a variety of platforms.  They can be found here.

ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.

Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with the help of calculations. 

Others

We also have experience with MOLPRO, AOMix, GAMESS, Mopac, NWChem and others.

QUANTUM MOLECULAR DYNAMICS

CPMD, CP2K, Siesta (Quantum Expresso)

The CPMD code is a plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab initio molecular dynamics. Its first version was developed by Jurg Hutter at IBM Zurich Research Laboratory starting from the original Car-Parrinello codes. 

CP2K and Siesta provide similar capabilities.  Quantum Expresso is a superset of Siesta that also allows the calculation of electron transport for nanoelectronic systems.

Reactive MD: ReaxFF

ReaxFF is a methodology for modeling chemical reactions with atomistic potentials based on the reactive force field approach developed by van Duin and coworkers. ReaxFF is freely available with the LAMMPS program from Sandia National Labs. SCM has also implemented ReaxFF as a commercial product.  Systems consisting of a 3D box of multiple molecules totaling tens of thousands of atoms can now be modeled on a modern desktop computer.

Parameters are included for many elements not included in traditional force fields, such as a number of transition metals. ReaxFF has been used over the past decade in various studies of inhomogeneous reactive systems, including solvent environments, interfaces, and molecules on metal and metal oxide surfaces.

More about the ReaxFF program