Learn More
A parallel message-passing implementation of a molecular dynamics (MD) program that is useful for bio(macro)mole-cules in aqueous environment is described. The software has been developed for a custom-designed 32-processor ring GROMACS (GROningen MAchine for Chemical Simulation) with communication to and from left and right neighbours, but can mn on any(More)
A method is presented that generates random protein structures that fulfil a set of upper and lower interatomic distance limits. These limits depend on distances measured in experimental structures and the strength of the interatomic interaction. Structural differences between generated structures are similar to those obtained from experiment and from MD(More)
In this paper we study the properties of pores formed by OmpF porin from Escherichia coli, based on a molecular dynamics simulation of the OmpF trimer, 318 palmitoyl-oleoyl-phosphatidylethanolamine lipids, 27 Na+ ions, and 12,992 water molecules. After equilibration and a nanosecond production run, the OmpF trimer exhibits a C-alpha root mean square(More)
We compared Molecular Dynamics simulations of a bilayer of 128 fully hydrated phospholipid (DPPC) molecules, using diierent parameters and macroscopic boundary conditions. The same system was studied under constant pressure, constant volume and constant surface tension boundary conditions, with two diierent sets of charges, the single point charge (SPC) and(More)
We simulated micelles of 40 (M40), 54 (M54), and 65 (M65) dodecylphosphocholine (DPC) lipids in water for up to 15 ns and analyzed the system energetics, structure of the water/lipid interface, structure and dynamics of the lipid tails, and overall size and shape of the micelles. M54 and M65 are similar, being mostly spherical in shape with comparable tail(More)
Molecular dynamics simulations allow a direct study of the structure and dynamics of membrane proteins and lipids. We describe the behavior of aromatic residues and lipid properties in POPE and POPC bilayer models with the Escherichia coli OmpF trimer, single alamethicin and Influenza M2 helices, 4-helix M2 bundles, and two alamethicin 6-helix channel(More)
A method is presented for a more efficient sampling of the configurational space of proteins as compared to conventional sampling techniques such as molecular dynamics. The method is based on the large conformational changes in proteins revealed by the "essential dynamics" analysis. A form of constrained dynamics is performed, forcing the system to move(More)
A comparison of a series of extended molecular dynamics (MD) simulations of bacteriophage T4 lysozyme in solvent with X-ray data is presented. Essential dynamics analyses were used to derive collective fluctuations from both the simulated trajectories and a distribution of crystallographic conformations. In both cases the main collective fluctuations(More)