Module 4 : A Case Study using Molecular Dynamics with NAMD

Lecture 20 : Input files in NAMD and VMD

OUTPUT

Temperature

Here the snapshot shows us the output of Instantaneous temperature with number of steps. The temperature specified in this run was 298.15 K. Here we notice fluctuations about the desired temperature to the range of +/-10%.

Cell Volume

Here we can observe a production run in NPT ensemble. The run initially starts with a higher cell volume, however the molecules readjusts because of the applied force field so that it remains nearly constant after 50,000 steps. It is after this region till 70,000 steps one can find the molar volume of a molecule.