|
|
|
|
|
|
|
|||||||||||||
|
|||||||||||||||||||
|
|||||||||||||||||||
GROMACS
|
|
|
|||||||||||||||||||||||||||||||||||||||||||
| > home > research > biochemistry > gromacs | ||||||||||||||||||||||||||||||||||||||||||||
|
|
||||||||||||||||||||||||||||||||||||||||||||
|
|
||||||||||||||||||||||||||||||||||||||||||||
|
|
||||||||||||||||||||||||||||||||||||||||||||
GROMACS |
||||||||||||||||||||||||||||||||||||||||||||
|
|
||||||||||||||||||||||||||||||||||||||||||||
GROMACS is a versatile package for performing molecular dynamics calculations, i.e. to simulate Newton's equations of motion for systems with hundreds to millions of particles. GROMACS is primarily designed for biochemical molecules like proteins and lipids that have a large number of complicated bonded interactions. GROMACS can also be used for non-biological systems, e.g. polymers.
The HPCx system currently has GROMACS versions 4.0, 3.3.3, 3.3.2, and 3.3.1 installed. The older version 3.2.1 can also be made available on request. New users are strongly recommended to use version 4.0 as this exhibits considerably better scaling than the 3.X versions. Existing users may also wish to migrate to version 4.0. Full details of the changes made to version 4.0 are given here.
A comparison of the performance of version 3.3.2 and version 4.0 for the D.DPPC benchmark is given by following figure:
D.DPPC benchmark for GROMACS versions 3.3.2 and 4.0
(Click for full-size image)
HPCx users may access GROMACS. To access this package you should mail the HPCx help desk and we will give you access to the executable.
Copies of the manuals for the different versions can be found here
A number of tutorials for GROMACS can be found here
| http://www.hpcx.ac.uk/research/biochemistry/gromacs.html | contact email - www@hpcx.ac.uk | © UoE HPCX Ltd |