Dear Justin, In the first tutorial You said "After we arrive at the correct temperature (based on kinetic energies), we will apply pressure to the system until it reaches the proper density." That is, you apply each NVT and NPT ensembles when you did the position restraints. Would not it only be sufficient to implement NPT ensemble on the system? Is it compulsory to apply both the x and y?
For example: I get proper density and stabilized the temperature of the system though I implement NPT ensemble on the system (not your tutorial sample). Thanks in advance -- Ahmet YILDIRIM
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