title: EntF*-D8
author: J. Vreede
description: molecular dynamics simulation of the EntF* peptide, residue 8 in D form -starting coordinates posre.gro: energy minimized and water+ions equilibrated around peptide -topology topol.top: force field AMBER99SB-ILDB, TIP3P water, protonation states at pH = 3 (E,K protonated), [NaCl] = 25 mM, disulfide bond generated between residues 14 and 6 -md settings md.mdp time step 2 fs, temperature = 298 K, pressure = 1 bar -1 microsecond trajectory dry.xtc, dry.gro frame rate 10 ps, water and ions removed, box centered on peptide -analysis files: radius of gyration, solvent accessible surface area (hydrophilic (backbone + hydrophilic side chains), hydrophobic (hydrophobic side chains)) 