title: All-atom molecular dynamics simulation of peptides
author: Ning Zhu
description: The initial structure was built using the LEaP module of AmberTools21, and we will run a total of 4000 minimization steps before starting to run molecular dynamics; 2000 is the steepest decline, followed by the conjugate gradient of 2000. That should be enough to clean up our structures. Then heat and equilibrate in three 250 ps stages: from heat 100 K to production temperature 300K, heavy atom position limiting, force constant decreasing from 10.0 to 1.0, then decreasing to 0.1 kcal/mol/Å2. The step size was set to 0.002 and the unconstrained production simulation was performed in an implicit generalized Bonn solvent (igb=8) in the canonical ensemble (NVT). The temperature was controlled by a Langevin thermostat (ntt=3) and molecular dynamics was performed for 200ns at a collision frequency of γ= 0.01 ps-1 (For implicit solvent, setting collision frequency to 0.01ps−1 can lead to significant, up to 100-fold in some cases, speedup of conformational sampling). Finally, the cpptraj module of AmberTools21 was used for combined clustering, RMSD, and other molecular dynamics trajectory analysis.