MDAnalysis

[…] obtained simply by counting the number of permeation events per pore50., vmd51 was used for analysis and trajectory visualization, including rendering of trajectory snapshots. the gromacs tools and mdanalysis49 libraries were used in the analysis scripts., the free energy along the pore axis for ammonia was calculated using awh52,53. awh is an enhanced sampling algorithm which, within a single […]

[…] of non-bonded contacts,using lennard-jones parameters. simulations were performed with an integration timestep of 2 fs., md simulations were analyzed using gromacs tools (hess et al., 2008), mdanalysis (michaud-agrawal et al., 2011), and locally written code. all images and animations were generated using pymol (delano, 2002)., strains used in this work are listed in table 2. for aq8a […]

[…] the stochastic component of the thermostat (bussi et al., 2007) would generate independent trajectories. in total, we simulated the dimer system for >10 µs., md trajectories were analyzed with mdanalysis (michaud-agrawal et al., 2011) and gromacs tools (hess, 2008). the distance d of the asp163–lys300 salt bridge was calculated as the minimum distance between the two carboxyl oδ1 and oδ2 […]