<jupyter_start><jupyter_text>Stage 2: Thermostat Equilibration (NVT)In this stage, the energy minimized structure is simulated using the NVT ensemble at 305K, which is skin temperature. The purpose of this stage is to equilibrate the thermostat and stablize the temperature fluctuations of the system. The see the input script (`nvt.mdp`) for details.<jupyter_code>!gmx grompp -f nvt.mdp -c ../1_em/confout.gro -p ../system.top -n ../index.ndx -o run.tpr -maxwarn 2
!gmx mdrun -s run.tpr<jupyter_output><empty_output>
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