8 files


posted on 14.08.2022, 09:16 authored by J. VreedeJ. Vreede

Molecular dynamics simulation of the EntF* peptide, residue 6 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))


Retention period