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GROMACS  
 
GROMACS
Description 
GROMACS (Groningen Machine for Chemical Simulations) is a versatile package which performs molecular dynamics, i.e. simulates 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.

A list of competitive features can be found at http://www.gromacs.org/content/view/12/176.

GROMACS calling structure is quite complicated, and it is not recommended that users proceed without at least becoming familiar with the program. The examples should be considered a guide and not a definitive step-by-step instruction set.

Official Homepage
      
Documentation
Users Manual
On-line Manual

License Agreement and Citation Format
License Agreement
GROMACS is Free Software, available under the GNU General Public License.

Citation Format 
Please cite these papers in the publication
  1. Berendsen, et al. (1995) Comp. Phys. Comm. 91: 43-56. 
  2. Lindahl, et al. (2001) J. Mol. Model. 7: 306-317.
  3. van der Spoel, et al. (2005) J. Comput. Chem. 26: 1701-1718.
  4. Hess, et al. (2008) J. Chem. Theory Comput. 4: 435-447.
 
How to Access the Program 
 
Availability
Servers Versions Paths Parallelization Methods
Fuji 4.0.7 /apps/Gromacs/gromacs MPI
       
Aurora 4.5.1 /apps/GROMACS/4.5.1 MPI
       
Axle 3.3.3 /apps/GROMACS/gromacs3 MPI
4.0.3 /apps/gpu/GROMACS-CUDA/current MPI, CUDA
4.0.3 /apps/GROMACS/gromacs4/ MPI
4.0.7 /apps/GROMACS/407 MPI
4.5.1 /apps/GROMACS/451 MPI
Using the Program
 
Additional Notes
 


Last Updated - 5th Oct 2011
 
     
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