8 files


posted on 14.08.2022, 09:20 authored by J. VreedeJ. Vreede

molecular dynamics simulation of the EntF* peptide, residue 12 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.groframe 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)) 


Retention period