title: EntF*-D2
author: J. Vreede
description: Molecular dynamics simulation of the EntF* peptide, residue 2 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 frame rate 1 ps radius of gyration, solvent accessible surface area (hydrophilic parts (backbone + hydrophilic side chains), hydrophobic parts (hydrophobic side chains))