Atomic and molecular simulation ((ab-initio , Gaussian,..)

Service description

Use of computational simulation methods in materials science research. We offer support and consulting on the study of thermal treatments, wetting, materials design, alloys, phase changes, electrical properties (e.g. conductivity, bandwidth) assignment of infrared, Raman, X-ray and neutron diffraction spectra, designing atomistic models that simulate the behaviour of the studied material at the macroscopic level.

Service description

Hydrogen effect within the iron lattice. The passive layer modeling, simulation of oxides.

Service description

Optimization and analysis of molecular structure We provide assistance in the full process from initial planning and project writing to final report elaboration and preparation of scientific publications. The analysis will be carried out in a progressive fashion, starting by the less expensive methods and evaluating progress at each step to decide if it is worth to continue with the following steps or which of them are worth to carry out. Currently, the service is able to carry out optimization calculations and fine electronic structure analyses for macromolecular systems (proteins, complexes or complexes with ligands). We can compute molecular orbitals and substrate reactivity in the active site of a protein or complex, and carry out analyses to determine the transition state considering the influence of the macromolecular environment, both in explicit and implicit solvent models. To carry out these analyses it is mandatory to obtain previous information regarding the system to simulate. Although the service will include the pertinent bibliographic searches in the analysis process, the more information that can be provided at the onset, the better. In addition, it is recommended that users get familiar with the system studied so that they can evaluate critically the results produced. Modeling incomplete parts of a molecule: - Retrieval of existing structures from databases (biological like PDB, drugs and chemicals like ZINC, geological crystallography like AMCSD, etc..). - Homology modelling of biological macromolecules - Threading - Modeling of missing loops - Addition of missing side chains - Ab initio structural modeling - Addition of H and charges Molecular Mechanics - Parameter generation for force fields when needed (e.g. ligands) - Energy minimization using molecular mechanics with an appropriate force field Molecular Dynamics - NVT equilibration - NPT equilibration - Production run - Trajectory analyses, movility, properties, representative conformations (clustering), etc... Simulated Annealing - Sucessive cycles of heating and cooling followed by final minimization Conformational search - Molecular Dynamics or SImulated Annealing - Trajectory analysis and selection of lowest energy conformers - Minimization of selected conformations SQM optimization - Addition of H - Optimization of H - Inspection of interactions (H-bridges, salt bridges, protonation states...) - Adjustment and additional optimizations Self-reference constrained optimization - Structural optimization constrained by the own structure as reference Unconstrained optimization Fine electronic structure analysis - Single point analysis to obtain relevant properties to the extent supported by the underlying technology (the most complete technology that can be used in a reasonable amount of time for the selected system shall be selected with the user) - Charge distribution analysis - Molecular orbital analysis - Frontier Molecular Orbitals - Reactivity analysis - Electronic Density - Energy calculations - Computation of excited states - Analysis of alternate states (isomers, tautomers...) Transition state search - Successive adjustments from substrates and products - saddle point calculations Technologies Force fields: depending on the type of molecules - AMBER, CHARMM, GROMACS (proteins, nucleic acids, when supported) - MMFF94, MFF94S, GAFF; OPLS-AA, UFF (for any atom) Depending on molecule size: - MM: GROMACS, OpenBabel, NAMD (macromolecules) - SQM, DFT: MOPAC20xx, SIESTA - Ab initio: GAMESS-US, NWChem, ORCA, MPQC, ErgoSCF, FreeON, Abinit, OpenDX, etc...