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EntF*-D15

dataset
posted on 14.08.2022, 09:22 authored by J. VreedeJ. Vreede

molecular dynamics simulation of the EntF* peptide, residue 15 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))   

History

Retention period

01/09/2032