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. 2021 Nov 2;6(45):30224–30240. doi: 10.1021/acsomega.1c01533

Table 2. Computational Details of MD and DPD Simulation.

(i) molecular dynamics (MD) simulation
Geometry Optimization
quality medium displacement 0.5 Å
algorithms smart maximum iteration 500
energy convergence 0.001 kcal/mol forcefield COMPASS
force 0.005 kcal mol–1 Å–1 charges forcefield assigned
truncation cubic spline spline width 1.0 Å
cutoff distance 12.5 Å buffer width 0.5 Å
van der Waals interaction atom-based electrostatic interaction group-based
Amorphous Cell Construction
lattice type cubic no. of configurations 10
temperature 298 K total density of final configurations 1.0 g/cc
Ewald accuracy 0.001 kcal/mol    
Blend Module (Mixing Task)
cutoff 12.5 Å energy samples 10 × 106
spline width 1.0 Å energy bin width 2.183 kcal/mol
algorithm smart cluster samples 1000
time step 1.0 fs iteration per cluster 20
simulation time 5.0 ps reference temperature 298 K
Forcite Module (Cohesive Energy Density Task)
quality medium total simulation time 5.0 ps
ensemble NVT thermostat Berendsen
time step 1.0 fs temperature difference 10.0 K
(ii) dissipative particle dynamics (DPD) simulation
bead density 3.0 interaction parameter 25.61
no. of beads 8142 beads bead mass 54 amu
time step 254.117 fs radius 3.23 Å in a physical unit
production run 5000 steps electrostatic interaction Ewald summation
initial velocities random configuration van der Waals interaction bead-based method
temperature 298 K (kBT = 1) truncation cubic spline
cutoff method 12.5 Å dissipation strength 0.08854 Å
spline width 1.0 Å dissipation radius 8.0 Å
buffer width 0.5 Å