Molecular dynamics simulation of a molecular model of the S. cerevisiae Sgt2-C (STI1) domain

Description

The system and trajectory of the relaxation of a structural model of Sgt2-C by all-atom molecular dynamics. In the accompanying paper, Sgt2-C is inferred to be a STI1 domain. Further details about the simulation protocols and results can be found within the accompanying paper and repository.

Files

Methods

In short, the protein model and solvent system (TIP3P, ~12k atoms, CHARMM36 [Huang & MacKerell, 2013]) once built was minimized (500 steps), slowly heated to 298K (0.01K/fs), and then simulated for 2 ns at constant volume twice: first with a 10 kJ/mol/Å2 harmonic restraint on each protein atom and then without restraints. The resulting system was equilibrated for 100 ns at constant pressure (1 atm). All manipulation and calculations were performed using VMD 1.9.2 [Humphrey, et al., 1996] and NAMD 2.11 [Phillips, et al., 2005].

Table of contents

Initial fully built system      2Q1_autopsf_tip3p_NaCl.pdb      2Q1_autopsf_tip3p_NaCl.psf Trajectory (100ns, sampled every 0.5 ns)      2Q1_autopsf_tip3p_NaCl.prod_tp.full100.dcd NAMD binary restart files      2Q1_autopsf_tip3p_NaCl.prod_tp35.restart.coor      2Q1_autopsf_tip3p_NaCl.prod_tp35.restart.vel      2Q1_autopsf_tip3p_NaCl.prod_tp35.restart.xsc

Other

Contact person: Ku-Feng (Geoffrey) Lin gufeng0602@gmail.com

Additional details