A novel protocol has been developed for comparing the structural properties of lipid bilayers determined by simulation with those determined by diffraction experiments, which makes it possible to test critically the ability of molecular dynamics simulations to reproduce experimental data. This model-independent method consists of analyzing data from molecular dynamics bilayer simulations in the...

We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy). This application programming interface (API) uses the ctypes python module that allows function calls to shared libraries, for example, written in C. To the best of our knowledge, this is the first reported interface to the GROMACS library that uses direct library calls....

1Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3 Theoretical and Computational Biophysics Dept., Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany 4Center for Biomembrane Research, Dept. Biochemistry & Biophysics, Stockholm University, SE...

Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. Gromita is a cross-platform, perl/tcl-tk based, interactive front end designed to break the command line barrier and introduce a new user-friendly environment to run molecular dynamics simulations through Gromacs. Our GUI features a novel workflow inter...

Silicon carbide nanotube (SiCNT) come forward in the great variety of nanotubes with higher durability until 1600 oC (in air) while carbon can stay stable 600 air). First five buckling loads single SiCNT placed between source and drain metal electrodes nano sized field effect transistors (FET) is investigated using two different molecular dynamics methods. L.A.M.M.P.S. software Gromacs package ...

Objective: The purpose of this study was to determine the structural-based molecular interactions between flavonoids contained in Acalypha indica L. and caspase-3 by docking dynamics (MD) simulations.
 Methods: In a computer simulation, ten A. were evaluated for using X-ray crystal structure human (PDB ID 1NME). AutoDock 4.2 software used docking, MD simulations done with GROMACS v2018.&#x...

The CELLmicrocosmos MembraneEditor (CmME) [1] enables researchers to generate PDB [2] based membrane structures in a convenient way. The lipid distribution is computed by algorithms working on the outer shapes of the molecules. For this reason, the computation and visualization process is very fast, while the atomistic structure of each single molecule remains unchanged. PDB membranes can be ex...