EntF*-D13

molecular dynamics simulation of the EntF* peptide, residue 13 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))