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Uso VMD, NAMD ENERGY
Calculo de Energias VDW, y Elec. Es necesario poseer .psf .pdb .dcd. y especificar los 2 componentes a medir. Basic Usage NAMDEnergy operates on either one or two selections; if only one selection is chosen, then internal energies for that selection will be calculated, whereas if two selections are chosen, only interaction energies between those […]
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TEST CCgenFF with Bencene molecule parte II con CHARMM-GUI
Se utilizó http://www.charmm-gui.org/?doc=input/pdbreader donde se agrego una molécula de benceno, con sus hidrogenos en formato PDB leyo la informacion del mismo luego Nos da esta informacion, donde buscamos el CSML, para ver si existen los parametros para esta molecula. Nos dice que esta, de dos formas la forma BENZ y la forma CHXE Asi que […]
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MDAnalysis
MDAnalysis documentation¶ Release: 0.19.2 Date: Nov 08, 2018 MDAnalysis (www.mdanalysis.org) is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, Amber, NAMD, LAMMPS, DL_POLY and other packages; it also reads other formats (e.g., PDB files and XYZ format trajectories; see Table of supported coordinate formats and Table of Supported Topology Formats for the full lists). It can write most of these formats, too, together with atom selections […]