Using the default settings for the simulation, the system will
first be energy minimized until convergence with a tolerance of
10 kJ/mol. Then the system will be heated to the user’s specified
temperature using Langevin integrator, and the density will be
adjusted using pressure coupling to 1 bar. Equilibration and pro-
duction simulations will be performed for the user’s specified num-
ber of steps, and the coordinates will be saved in constant intervals
(as specified by user) into the trajectory file (netcdf format). All
protein heavy atoms and ligand heavy atoms (if present) are har-
monically restrained (spring constant is user-defined).3.5 Perform WATsite
Analysis
In this step, we will perform WATsite analysis on the trajectory file
generated in the previous step (Fig.5). The amber topology (pro-
t_amber.prmtop) and coordinate (prot_amber.inpcrd) files gener-
ated instep 2, as well as the trajectory (sys_md.nc) file generated
instep 4should be specified correctly.
The number of steps and water model used for WATsite analysis
need to be identical to those used during the production simula-
tion. Clustering algorithm used to predict hydration site locations
from water density can also be chosen (seeNote 5).Fig. 4 Step 3of WATsite procedure to specify parameters for running the MD simulations via OpenMM
Calculation of Water Thermodynamics 395