TS :                                         Number of steps .This is written after every 100 steps
BOND:                                     Refers to the energy by bond contribution
ANGLE:                                    Refers to the energy by angle contribution
DIHED:                                    Refers to the energy by dihedral contribution
IMPR:                                      Refers to the energy by improper contribution
ELECT:                                    Refers to the energy by Electronic contribution
VDW:                                      Refers to the energy by vdW(i.e LJ) contribution
TEMP/TEMPAVG:                   Temperature in K
TOTAL2/TOTAL3:                  Indicates the total energy

After the simulation is run, then comes the analysis part. Visual Molecular Dynamics (VMD) is a convenient tool for displaying, animating, and analyzing large systems using 3-D graphics and built-in scripting    ( http://www.ks.uiuc.edu/Research/vmd/). Here one can view the trajectory i.e ‘.dcd’ file .The other forms of Energy and thermodynamic properties can also be  viewed easily. The steps are as follows:

Step I: Load the trajectory and the PDB file

Here the ‘frames’ indicate the number of steps of the simulation.

STEP II: Select the Plotting tool

STEP IV: Plot the desired property with respect to number of steps or time