Dynarepo 1W1W

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003G7

Created: 19 Jul 2025
License: Apache License 2.0 (opens in a new tab)

Description

single chains from test53, Classical MD simulations, 3 replicates of 500 ns

Molecular system

Starting structure: 1W1WPDB 1W1W(opens in a new tab)
Force field: CHARMM36mTIP3P
Engine: GROMACS 2024.2
Method: Classical MD
Ensemble: NPT
Temperature: 310 K
Timestep: 2 fs
Composition: Molecules of interest
ProteinProtein · 1 chain6,834 atoms427 residues
Total6,834 atoms427 residues
Box dimensions: Dodecahedron
a14.434nm
b14.434nm
c10.235nm

Sequences

Sequence 1Protein · 427 residues

GRLVGLELSN FKSYRGVTKV GFGESNFTSI IGPNGSGKSN MMDAISFVLG VRSNHLRSNI LKDLIYRGVL NDENSDDYDN EGAASSNPQS AYVKAFYQKG NKLVELMRII SRNGDTSYKI DGKTVSYKDY SIFLENENIL IKAKNFLVFQ GDVEQIAAQS PVELSRMFEE VSGSIQYKKE YEELKEKIEK LSKSATESIK NRRRIHGELK TYKSPGLEVL FQGPRGSRYD EAEGRFEVIN NETEQLKAEE KKILNQFLKI KKKRKELFEK TFDYVSDHLD AIYRELTKNP NSNVELAGGN ASLTIEDEDE PFNAGIKYHA TPPLKRFKDM EYLSGGEKTV AALALLFAIN SYQPSPFFVL DEVDAALDIT NVQRIAAYIR RHRNPDLQFI VISLKNTMFE KSDALVGVYR QQQENSSKII TLDLSNY

Run	Outputs
replica 1	Trajectory Analyses
replica 2	Trajectory Analyses
replica 3	Trajectory Analyses

Files

43 files

All files

trajectory.binBIN
pca_trajectory_01.binBIN
pca_trajectory_02.binBIN
pca_trajectory_03.binBIN
pca_trajectory_04.binBIN
pca_trajectory_05.binBIN
pca_trajectory_06.binBIN
pca_trajectory_07.binBIN
pca_trajectory_08.binBIN
pca_trajectory_09.binBIN

Dynarepo 1W1W

Description

Molecular system

Sequences

Experiments

Files

Contributors

Acknowledgements