A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

Abstract

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However, performing a successful simulation requires sufficient computational resources, familiarity with the simulation software, and experience in the setup of a system and the analysis of the resulting trajectories. These considerations become especially critical in large-scale parametric MD simulations. Offering such tools to a wide user community requires a robust and versatile, but user-friendly, facility for molecular dynamics simulations with access to vast computational resources. Here, we present the GROMACS grid-enabled Web portal for the setup and execution of molecular dynamics simulation on the WeNMR grid infrastructure, a distributed network of computational resources within the European Grid Initiative. The Web portal aims at ease-of-use through automated setup of the simulation system using bestpractice protocols, yet allowing for tuning of key parameters. Alternatively, the simulation can be started from preconfigured GROMACS simulation systems. Performing multiple lengthy calculations using multiple processors on the WeNMR grid infrastructure ensures scalability. The combination of analysis routines for quality assurance and automatic recovery in case of failures provides a reliable platform for MD simulations. The GROMACS Web portal is embedded within the services of the WeNMR Virtual Research Community (VRC) accessible from http://www.wenmr.eu/wenmr/nmr-services. It is freely accessible upon registration with a valid X509 personal certificate with the enmr.eu Virtual Organization (VO).

Effect of chrysin omega‐3 and 6 fatty acid esters on mushroom tyrosinase activity, stability, and structure

“…In the next step, the system was balanced at a constant temperature of 310 K and a constant pressure of 1 bar for 50 ps. Molecular dynamics calculations were performed for 5 ns using GROMACS software (Van Dijk, Wassenaar, & Bonvin, ).…”

Perspective on the Martini model

“…To harvest this enormous power, automated workflows should be designed and optimized. Efforts in that direction are already undertaken in a number of groups, for example in the grid-enabled web portal for MD simulations, 340 automated topology builder 341 and automatic embedding of membrane proteins. 342 To facilitate the Martini workflow, we have developed the Martinize script 15 which generates GROMACS topology files for proteins from coordinate input files.…”

Sucrose Nonfermenting 1-Related Protein Kinase 1 Phosphorylates a Geminivirus Rep Protein to Impair Viral Replication and Infection

“…Default High Ambiguity Drive Docking (HADDOCK) parameters were used throughout the docking procedure on the Web server (van Dijk et al, 2012;van Zundert et al, 2016) with the following exceptions: auto_passive_ radius = 6.5, create_narestraints = True, rotate180_0 = False, crossdock = True, and calcdesolv = True. Active residues for Rep(7-122) were defined as Arg-7, Lys-68, Arg-94, Ala-95, Lys-96, and Ser-97, and active bp corresponding to the Rep binding site (Fig.…”