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. Author manuscript; available in PMC: 2012 Mar 28.
Published in final edited form as: J Chem Inf Model. 2011 Mar 3;51(3):635–646. doi: 10.1021/ci100355c

Table 1.

Parameters used for the MD equilibration and production runs

Steps Timestep Harmonic Constraints (kcal/mol/Å2)
Numstep Temperature Backbone Ligand Side Chains Lipids Water and Ions Temperature Control
Heating
1 2.0 fs 100 ps 300 K 50 50 50 50 50 NVT
Equilibration Steps
2 2.0 fs 100 ps 300 K 50 50 50 50 50 NPT
3 2.0 fs 100 ps 300 K 50 50 50 50 10 NPT
4 2.0 fs 100 ps 300 K 50 50 10 10 5 NPT
5 2.0 fs 100 ps 300 K 50 10 5 5 1 NPT
6 2.0 fs 100 ps 300 K 50 5 1 1 - NPT
7 2.0 fs 100 ps 300 K 25 - - - - NPT
8 2.0 fs 100 ps 300 K 10 - - - - NPT
9 2.0 fs 100 ps 300 K 5 - - - - NPT
10 2.0 fs 250 ps 300 K 1 - - - - NPT
Production Run
11 2.0 fs 20 ns 300 K - - - - - NPT P=1.0132 bar
T = 300 K