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<td>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, lipids and nucleic acids 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.</td>
<td>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.</td>
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<td>NAMD
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<td>NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code.
<td>NAMD is a widely used molecular dynamics application designed to simulate bio-molecular systems on a wide variety of compute platforms.
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-[Build & run instructions, details about the benchmarks](./gadget/4.0/README.md)
# GROMACS <a name="gromacs"></a>
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, lipids and nucleic acids 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. In GROMACS 4.6 and up, on almost all common computing platforms, the innermost loops are written in C using intrinsic functions that the compiler transforms to SIMD machine instructions, to utilize the available instruction-level parallelism. These kernels are available in either single and double precision, and in support all the different kinds of SIMD support found in x86-family (and other) processors.
- Also since GROMACS 4.6, we have excellent CUDA-based GPU acceleration on GPUs that have Nvidia compute capability >= 2.0 (e.g. Fermi or later)
- 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 a 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.
- 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-ness, and can thus be read by any version GROMACS, even if it was compiled using a different floating-point precision.
- 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 either the standard MPI communication protocol, or via our own “Thread MPI” library for single-node workstations.
- 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 aminoacid residues as well as some modified ones, the 4 nucleotide and 4 deoxinucleotide resides, 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 Lesser General Public License (LGPL), version 2.1. You can redistribute it and/or modify it under the terms of the LGPL as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
Instructions:
- Web site: http://www.gromacs.org/
- Code download: http://www.gromacs.org/Downloads The UEABS benchmark cases require the use of a 2020 or newer versio.
- Test Case A: https://repository.prace-ri.eu/ueabs/GROMACS/2.2/GROMACS_TestCaseA.tar.xz
- Test Case B: https://repository.prace-ri.eu/ueabs/GROMACS/2.2/GROMACS_TestCaseB.tar.xz
- Test Case C: https://repository.prace-ri.eu/ueabs/GROMACS/2.2/GROMACS_TestCaseC.tar.xz
- Build and Run Instructions : https://repository.prace-ri.eu/git/UEABS/ueabs/-/blob/r2.2-dev/gromacs/README.md
# NAMD <a name="namd"></a>
NAMD is a widely used molecular dynamics application designed to simulate bio-molecular systems on a wide variety of compute platforms. NAMD is developed by the “Theoretical and Computational Biophysics Group” at the University of Illinois at Urbana Champaign. In the design of NAMD particular emphasis has been placed on scalability when utilizing a large number of processors. The application can read a wide variety of different file formats, for example force fields, protein structure, which are commonly used in bio-molecular science.
A NAMD license can be applied for on the developer’s website free of charge. Once the license has been obtained, binaries for a number of platforms and the source can be downloaded from the website.
Deployment areas of NAMD include pharmaceutical research by academic and industrial users. NAMD is particularly suitable when the interaction between a number of proteins or between proteins and other chemical substances is of interest. Typical examples are vaccine research and transport processes through cell membrane proteins.
NAMD is written in C++ and parallelised using Charm++ parallel objects, which are implemented on top of MPI.
