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Documentation FAQs How-tos Tutorials Molecular dynamics simulation using Gromacs 1pf4.pdb Human eIF3k: Crystal structure 1rz4 from PDB has 2 missing residues Filled in 2 missing loop residues using modloop (Modeller). Modloop also fills in missing atoms for GLN 119, ASP 182 and GLU 183. Protein with all missing atoms and residues filled in Links Quick links University Library MyUCDavis Search this site Genome Center Patrice Koehl's research web site Room 4319, Genome Center, GBSF University of California Davis 451 East Health Sciences Drive Davis, CA 95616 (530) 754 5121 phone (530) 754 9658 fax

Patrice Koehl's research web site > Documentation > Tutorials > Molecular dynamics simulation using Gromacs Personal tools Log in Molecular dynamics simulation using Gromacs summary All content on one page (useful for printing, presentation mode etc.) About Energy Minimization in Gromacs Steepest Descent, Congugate Gradient, Limited-memory Broyden-Fletcher-Goldfarb-Shanno MD step1: Prep the protein before solvating Fill in missing residues, atoms. Follow with enerrgy minimization. MD step2: Solvate the protein Generated solvent containing 102645 atoms in 34215 residues, follow with energy minimization MD step3: Position Restrained MD The positions of the protein atoms are held constant while the water is permitted to equilibite into cavities MD step4: Production MD prep is over, now the actual simulation of trajectories of the atoms in the solvent environment. Hints if problems are encountered Attached files 1pf4.pdb

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