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This article describes the collisional dynamics (CD) method adapted for molecules with geometrical constraints within a description using Cartesian coordinates for the atoms. In the CD method, stochastic collisions with virtual particles are included in usual molecular dynamics simulations to couple the considered polymer molecule to a solvent. The actual(More)
We have studied the mechanical properties of the immunoglobulin-binding domain of protein G at the atomic level under stretching at constant velocity using molecular dynamics simulations. We have found that the unfolding process can occur either in a single step or through intermediate states. Analysis of the trajectories from the molecular dynamic(More)
The calculation of diffracted intensities from an atomic model is a routine step in the course of structure solution, and its efficiency may be crucial for the feasibility of the study. An intense X-ray free-electron laser (XFEL) pulse can change the electron configurations of atoms during its action. This results in time-dependence of the diffracted(More)
The amyloidogenic peptide VDSWNVLVAG from Bgl2p-glucantransferase of Saccharomyces cerevisiae cell wall and its modifying analog VESWNVLVAG were taken for the construction of four types of bilayers which differ by orientation of the peptides in the layers and of the layers relative to each other. These bilayers were used as starting models for the molecular(More)
Mechanical properties of proteins are important for a wide range of biological processes including cell adhesion, muscle contraction, and protein translocation across biological membranes. It is necessary to reveal how proteins achieve their required mechanical stability under natural conditions in order to understand the biological processes and also to(More)
Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such(More)
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