Here you will do a equilibration of ubiquitin in vacuum for 500 fs.

Look at the NAMD input file equil.conf, you will:

1. Use the restart files from a pre-simulation:
# Continuing a job from the restart files
set inputname      common/ubi_equil
binCoordinates     $inputname.restart.coor
extendedSystem	   $inputname.xsc

and 

binvelocities 	    $inputname.restart.vel


2. Use 1fs as your time step:
timestep            1.0  ;# 1fs/step


When you finish the simulation, you will:

1. Get the temperature file by typing:
gettemp youroutputfile > temp1.dat

2. Use Matlab to analyze your data:
First type: 

matlab -nosplash &

in a terminal. The matlab workplace will start.
Then in the Matlab command window type:

data_analysis

This will calculate the temperature autocorrelation
function and fit it into an exponential function
(y=exp(-t/tau0).
Both of them will be shown in a Figure window.

The fitting parameter tau0 will be the output in the Matlab command
window. This number will be used in your later analysis.

The autocorrelation function will be saved as: auto_tmp.dat.
tau0 will be saved as tau0.dat.

