title: Hundred nanosecond molecular dynamics simulation of the G domain of K-Ras4B
author: Sander Roet
description: (This is a public copy of https://figshare.com/s/453b1b215cf2f9270769)This is a one hundred nanosecond simulation of the G domain of K-Ras4B (UNIPROT:P01116-2, residues 1-166). The simulation was generated using GROMACS v.4.6.5 with the AMBER99SB-ILDN forcefield (altered following doi:10.1002/jcc.10262, see References), TIP3P water and 0.15 M salt. The leap-frog integrator with 2 fs timestep was used. A v-rescale thermostat was used at 310 K, with two energy groups (protein+GTP+MG and water+salt) and a time constant of 0.1 ps. PME was used with a tolerance of 1e-5 for the coulomb interactions and a cutoff was used for the VdW interactions, both with a cutoff of 1.1 nm. A Parrinello-rahman barostat was applied with a reference pressure of 1 bar and a time constant of 1 ps. For more information take a look at md.mdp. Coordinates were saved every 1 nanosecond and waters were stripped, resulting in a trajectory of 101 snapshots. The initial model was made using the G-domain of GppNHp bound H-Ras (PDB ID: 4EFL). The protein was converted using MODELLER v9.16(doi:10.1002/cpbi.3 , see References) and GppNHp was converted to GTP by hand.