I am simulating a protein in water with Gromacs  and I can use Gnuplot in order to plot my graphs.I have two columns of data..x values are related to the time of  simuIation and y values are related to one of my system's variable which can be investigated after plotting the curves. number of x and y values are more than 1000.and and i want to run averave in my curves I know what these fluctuations mean.I use this command:

plot "pressure.xvg" u 1:2 w l lt 6 title "pressure-300k"

it gives me the graph without the red line in the example.i need the command to add it too

yes.we use that abbreviation.

my purpose of "average" is just that red line which has been shown in that example gragh.

what does $1 and $2 and $3 mean?are they values in data column?

I know that we can estimate "the average" just by looking at the graph (those fuzzy spiky lines) and find middle of Vertical lines, but i do not know how to plot it.if I send you my pressure.xvg can you open it in linux and have a look please? 

Hello and thanks again for your time. I talked to my supervisor and asked her to explain that red line. 

Ok, the red line is named the running average of the simulation data. In fact the black fuzzy graph shows the changes of a parameter with the simulation time. The red line corresponds to the instant running average of that data. Only I wanted to know what is the command line in gnuplot to ask the program to draw that line for me?

Hi,

look at this.

http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/analysis_MD1.html

As the curve is fluctuating a lot, it remains still difficult to estimate how many times the curve gets through the line "Threshold". To overcome this problem, we can perform a "running average". For this, in "Data" menu, click on "Transformations" and in the drop-dowwn menu, on "Running averages...". Select the set S0, then the "median" running and put 50 in the "Length of the average". Close the frame after clicking on the "Accept" button.

"Select the set S0, then the "median" running and put 50 in the "Length of the average". Close the frame after clicking on the "Accept" button."

Now, where is the average value? Only there is a red line in pressure.xvg

For exemple in the case of lysozyme,  the average value of the pressure is 1.05 bar

dear Fatemeh Rasavi,

there is the same thread in stack overflow:

https://stackoverflow.com/questions/42855285/plotting-average-curve-for-points-in-gnuplot?answertab=votes#tab-top

There, the very good script of maij, answers your question specifically.

Rename your 'pressure.xvg' file to 'test.data' and run the script of the link.

For the data you posted, using n=50 gives you a 10 ps running average, which is exactly what you asked (i.e, the gromacs example of lysozyme in water).

regards,