Molecular Dynamics Package
GROMACS is a versatile and extremely well optimized package to perform
molecular dynamics computer simulations and subsequent trajectory
analysis. It is developed for biomolecules like proteins, but the
extremely high performance means it is used also in several other field
like polymer chemistry and solid state physics. This version has the
dynamic libs and executables; to hack new utility programs you also
need the headers and static libs in gromacs-dev. Linux kernel 2.4 or
later is STRONGLY recommended on Pentium III and later processors since
GROMACS then can use assembly loops with SSE instructions.
- Developed at science
- Sources inherited from project openSUSE:Factory
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Source Files
| Filename | Size | Changed |
|---|---|---|
| gromacs-4.6.tar.bz2 | 0005392564 5.14 MB | |
| gromacs.changes | 0000010073 9.84 KB | |
| gromacs.spec | 0000003805 3.72 KB |
Revision 22 (latest revision is 59)
Stephan Kulow (coolo)
accepted
request 150933
from
Dmitry Roshchin (Dmitry_R)
(revision 22)
- Update to 4.6
New features
- New Verlet non-bonded scheme which, by default, uses exact cut-off's
and a buffered pair-list.
- Multi-level hybrid parallelization (MPI + OpenMP + CUDA):
full OpenMP multithreading with the Verlet scheme;
- OpenMP mulitthreading for PME-only nodes with the group scheme;
native GPU acceleration using CUDA (supporte NVIDIA hardware).
- New x86 SIMD non-bonded kernels for the usual cut-off scheme, called
group scheme and the new verlet scheme, use x86 SIMD intrinsics (no
more assembly code):
SSE2
SSE4.1
AVX-128-FMA (for AMD Bulldozer/Piledriver)
AVX-256 (for Intel Sandy/Ivy Bridge)
- Automated OpenMP thread count choice to use all available cores.
- Automated CPU affinity setting: locking processes or threads to cores.
- Automated PP-PME (task) load-balancing: balancing non-bonded force and
PME mesh workload when the two are executed on different
compute-resources (i.e CPU and GPU or different CPUs). This enables
GPU-CPU and PP-PME process load balancing by shifting work from the
mesh to the non-bonded calculation.
- PPPM/P3M with analytical derivative at the same cost and with the same
features as PME.
- New, advanced free energy sampling techniques.
- AdResS adaptive resolution simulation support.
- Enforced rotation ("rotational pulling")
- Build configuration now uses CMake, configure+autoconf/make no longer
supported. (The CMake build system features with a lot of automation
and cleverness under the hood and we know that the it might not always (forwarded request 150931 from kwk)
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