MDAnalysis

[…] mutant nbds using gromacs with charmm36m force field,. for simulation details see the supplementary materials. analysis was performed by employing gromacs tools, vmd network wizard plugin, and the mdanalysis python package., the datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request., , boglárka zámbó, zsuzsa […]

[…] threshold, t. note that distances must be calculated taking into account the periodic boundary conditions of the simulation box. all the distance matrices were computed using the python package mdanalysis. for each of the statistically independent snapshots of the system, we evaluated the contact matrix. the final matrix, h, is given by the sum of the contact matrices for each snapshot., […]

[…] parameters, with a verlet cutoff scheme to permit gpu calculation of non-bonded contacts. simulations were performed with an integration time step of 2 fs. the mds were analyzed using gromacs tools, mdanalysis and locally written python and perl scripts., homologous sequences were identified in the uniprotkb database, using eight iterations of jackhmmer, with the default search parameters. […]

[…] that f(r) = 0 for large distances, so that the above integral converges, which can be ensured by adding a suitable constant to f(r)., visualization was done using vmd, and analysis was done using mdanalysis., to determine the free energy surface for glycophorin dimerization, we perform umbrella sampling simulations of the dimer along the interhelical drms coordinate as described […]

[…] order and thickness maps were generated using tools developed by n. castillo et al.. the partial density map of a patch of a membrane was calculated using an in house script which utilized the mdanalysis, python module. the script was written to mimic the functionality of the gmx density gromacs tool, but could also analyze subsets of a system which do change size over time. the partial […]

[…] was followed by a 1150 ns production stage for each system., trajectories were analyzed with the mint package [], ptraj module from ambertools 1.5 [] and in-house written python scripts employing mdanalysis library []. the criteria for the presence of hydrogen bonds were: 3.5 å for the maximal acceptor-donor distance and minimal acceptor-hydrogen-donor angle was set to 150 degrees. the base […]