Benchmarks 
Gromacs
Gromacs
Gromacs
Last Updated on Friday, 25 November 2011 13:21 Written by Jordi Blasco Friday, 16 April 2010 18:53
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.
Official website : http://www.gromacs.org
| Test name | Version | Type | Description |
| XRQTC.Gromacs_9LDT | 2010.4 | DFT | Molecular dynamics with explicit water of the protein structure 9LDT. It is a tetramer with a Mw of 74822 Da. Using LINCS, periodic boundary conditions, and PME and a switched cut-off for Lennard-Jones interactions of 0.9 nm. Total number of atoms: 90393. 100000 time step of 0.002 ps amounting a total of 200 ps. Benchmarck provided by Dr. Ramon Crehuet (CSIC) |
| XRQTC.Gromacs_DSPC | 2010.5 | DSPC | Molecular dynamics of a hydrated lipid bilayer using Gromacs 4.0.7. The simulated system consists in 6186 explicit water molecules and a DSPC bilayer with 64 lipid molecules at each leaflet. Periodic boundary conditions, LINCS constraint algorithm and 1nm for the cutoff for van der waals interactions are used. The time step is 2fs and the total simulation times is 1ns. Benchmarck provided by Dr. Ramon Reigada (IQTC-UB) |
