NMR refinement and peptide folding using the GROMACS software.

Nuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins and nucleic acids. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package it is possible to model distance restraints, dihedral restraints and orientation restraints. The output from the script is validated by performing simulations with and without restraints, including the ab initio refinement of one peptide.

Structural studies of melting on the picosecond time scale.

Ultrafast structural studies of laser-induced melting have demonstrated that the solid-liquid phase transition can take place on a picosecond time scale in a variety of materials. Experimental studies using ångström wavelength X-rays from the sub-picosecond pulse source at Stanford (now retired) on non-thermal melting of semi-conductors, such as indium antimonide, employed the decay of a single Bragg-peak to measure the time component of the phase transition. These materials were found to start melting within one picosecond after the laser pulse. Recent computer simulations have described the thermal melting of ice induced by an infrared laser pulse. Here it was shown that melting can happen within a few picoseconds, somewhat slower than non-thermal melting in semi-conductors. These computer simulations are compatible with spectroscopy experiments on ice-melting, demonstrating that simulations form a very powerful complement to experiments targeting the process of phase-transitions. Here we present an overview of recent experimental and theoretical studies of melting, as well as new simulations of ice-melting where the effect of the size of the crystal on scattering is studied. Based on simulations of a near-macroscopic crystal, we predict the decay of the most intense Bragg peaks of ice following heating by laser pulse, by modeling the scattering from the melting sample in the simulations.