MDAnalysis

[…] other simulation packages, such as amber, charmm and namd after conversion of the md trajectory to the gromacs format (.xtc or.trr file). this can be achieved with several tools such as wordom , the mdanalysis package and the catdcd plugin (http://www.ks.uiuc.edu/development/mdtools/catdcd/). the user can employ the gromacs tool editconf to convert the pdb file of the starting structure, or one […]

[…] initial structure by the d0 helices (which had been kept rigid during the modeling process), and cα rmsds calculated between the aligned, modeled loop and the initial structure using the mdanalysis package []. structural figures and movies were generated using vmd 1.9.3 []., bacterial strains and plasmids used in this study are listed in additional file . the following strains […]

[…] method was used to constrain all bond lengths, and a 2 fs integration step was used. the simulations were carried out using gromacs (v5.0.5) and the analyses were performed using python and the mdanalysis libraries. all molecular images were created using vmd., data were analyzed by one-way anova followed by bonferroni multiple comparisons tests or by two-tailed student’s t-test (graphpad […]

[…] permit gpu calculation 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 (), mdanalysis (), and locally written code. all images and animations were generated using pymol ()., strains used in this work are listed in . for aq8a strains, a gln8ala mutation was introduced […]

[…] as implemented in ambertools14 (). interaction energies between waters referred to as w1-4 in the text and the binding pocket residues of pb1(5) and brd4(1) were analyzed using the python toolkit mdanalysis () and the gromacs tools. four spherical hydration sites with 1.2-å radius were defined and centered on the crystallographic water coordinates; for pb1(5), the water positions were taken […]

[…] 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 […]