GROMACS—the road ahead

Abstract

Molecular dynamics (MD) simulations form a powerful tool that is complementary to experiments and theory. They allow detailed investigations of both biological and chemical systems at the atomic level at timescales ranging from femtoseconds to milliseconds. Mechanisms and processes not accessible to experimental techniques can be followed in ‘real time’, and hypotheses based on experiments or theoretical arguments can be tested. Limits on the accuracy of results are mainly due to the physical models, the ratio of the complexity of the problem and the amount of computer time. Here, we review the state of the art in MD simulations with a focus on imminent challenges for the GROMACS (GROningen MAchine for Chemical Simulation) software. New hardware puts new requirements on software, while the breadth of applications and the amount of physical models implemented are increasing rapidly, highlighting shortcomings in the architecture of the programs. We sketch a road map for a popular scientific software package and discuss some of the choices to be made. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 710–715 DOI: 10.1002/wcms.50 This article is categorized under: Software > Molecular Modeling

Does the Like Dissolves Like Rule Hold for Fullerene and Ionic Liquids?

“…47 All large-scale simulations were carried out using the GROMACS 4 software package. [48][49][50][51] Fullerene C 60 is nearly insoluble at 300 K. Although the well-ordered periodic structure of the solid phase changes to clusterlike ( Figure 4), no fullerene is present in dissolved state ( Figure 5) 4 ] becomes outstandingly successful upon just 20 K temperature increase, 5 g l -1 (310 K), 49 g l -1 (320 K), > 66 g l -1 (333 K). Since enthalpic factor does not change significantly between 300 and 320 K, 9 the dissolution is boosted due to entropic factor increase.…”

Thermodynamics of hydronium and hydroxide surface solvation

“…Here, the polarization energy of solute and water were attributed to solute-water and water-water interactions, respectively. Simulations were carried out using the efficient GROMACS simulation software [59,60], further details are given in refs. [5,6] and in the supporting information.…”

The effect of temperature on the compressive buckling of boron nitride nanotubes

“…Our simulation tool is classical MD 51, which predicts the motion of the atoms of a system being studied, by numerically integrating the equations of motion governed by interatomic interaction. In the present work, we use GROMACS MD software package 52–56 to perform the simulations. The potential energy related to the atomic interactions is expressed as the sum of bonded and nonbonded interaction terms …”