Here you will quench the temperature to 0K for the second time.
Again this is realized in the NAMD input file echo.conf as

set temperature    0
temperature         $temperature

Remember to set tau at the very beginning,

set tau 200        ;# here you want to assign your tau value

and you will simulate it for tau time steps. 
The temperature data can be get by:

gettemp youroutputfile > temp3.dat

Now copy the previous data temp1.dat and temp2.dat to
this directory:

cp ../01_equil_NVE/temp1.dat
cp ../02_quencha/temp2.dat

and combine them to make the whole trajectory 

cat temp[1-3].dat > temp.dat

It is important to name the file as temp.dat, since by default
it is assumed in the Matlab script cmp_echo.m.

Once it is done, you start Matlab by typing:

Matlab -nosplash &

Now load temp.dat into Matlab. Type:

load temp.dat

You can plot it by typing:

plot(temp(1,:), temp(2,:))

You will see two sharp dips corresponding to the first and the 
second quench you did. But you also expect to see a third dip,
this is the echo. If you don't have it, you need to check your
data.

Now we want to compare it using the harmonic approximation.
To do this, input your tau first. Type:

tau= the number you are assigned

Then type:

cmp_echo(tau,temp)

This will pop up a window with a simulated echo plot as well 
as the one from the harmonic approximation. You are able to 
see how good the approximation is.

Get the depth of the echo by typing in the Matlab command window:

75 - min(temp(510+tau:end,2))

Input your tau and this number into the webpage on your tutorial.
Different values from all students will be collected and fitted
to an exponential function. From that you can get the dephasing
time.

So far you are doing a great job. If you have more time, you can go
to the last two folders to try a constant velocity assignment echo.
