| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T74 |
0-92 |
Sentence |
denotes |
In total, 5000 steps of energy minimizations were done using the steepest descent algorithm. |
| T75 |
93-247 |
Sentence |
denotes |
In all steps, the LINCS algorithm was used to constrain all bonds containing hydrogen atoms and a time step of 2 fs was used as the integration time step. |
| T76 |
248-306 |
Sentence |
denotes |
Equilibration of all systems was performed in three steps. |
| T77 |
307-683 |
Sentence |
denotes |
In the first step, 100,000 steps of simulation were performed using a velocity-rescaling thermostat to maintain the temperature at 310 K with a 0.1 ps coupling constant in an NVT ensemble under periodic boundary conditions and harmonic restraints on the backbone and side-chain atoms of the complex.38 A velocity rescaling thermostat was used in all other steps of simulation. |
| T78 |
684-1004 |
Sentence |
denotes |
In the next step, we performed 300,000 steps in the isothermal-isobaric NPT ensemble at a temperature of 310 K and pressure of 1 bar using a Berendsen barostat.39 This was done through decreasing the force constant of the restraint on the backbone and side-chain atoms of the complex from 1000 to 100 and finally to 10 . |
| T79 |
1005-1125 |
Sentence |
denotes |
The Berendsen barostat was only used for the equilibration step because of its usefulness in rapidly correcting density. |
| T80 |
1126-1263 |
Sentence |
denotes |
In the next step, the restraints were removed, and the systems were subjected to 1,000,000 steps of MD simulation under the NPT ensemble. |
