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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))