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3 Running MD

3.3 Equilibration of Implicit Solvent System (GB)

This tutorial is under development.

It will eventually have inputs for equilibrating an implicit solvent system as was outlined in:
Nguyen, H., Maier, J., Huang, H., Perrone, V. and C. Simmerling, Folding Simulations for Proteins with Diverse Topologies are Accessible in Days with Physics-Based Force Field and Implicit Solvent, J. Am. Chem. Soc., 2014, 136(40), 13959–13962.

Please check back in the future.

Equilibration Protocol (from Supplementary Information)
Initial structures were built using the LEaP module of AmberTools17 then minimized and equilibrated in three 250 ps stages: heating from 100 K to the production temperature with heavy atom positional restraints of 10 kcal mol-1 Å-2, reducing force constant from 10.0 to 1.0 and then to 0.1 kcal mol-1 Å-2. A time step of 4 fs was used with hydrogen mass repartitioning. Bonds involving hydrogen were constrained by the SHAKE algorithm with a tolerance of 0.00001. Temperature was controlled with a Langevin thermostat with collision frequency γ = 1.0 ps-1. We used 300 K.