Dear all,
I want to calculate ACF of radius of gyration using gmx gyrate. I used the following command:
gmx gyrate -f npt3.xtc -s npt3.tpr -o gyrate.xvg -acf gyrateacf.xvg -n molindex.ndx -b 0 -e 50000
and it gave me the the plot like I attached here. First, I asked for 0 to 50000 (ps) but it gave me 0 to 2500 (ps). Why?
second. I asked for just polymer molecule ACF of Rg but there are three plots. I can not distinguish that plots. Which plot can be used for polymer ACF of Rg?
Thanks
Dear Mohammad Rezayani
Aren't the 3 components the raddi of gyration with respect to x, y and z? So you should have 3 ACFs, one per axis
Dear Nicola Piasentin
Thank you very much for your reply.You are right.
Do you have any Idea for time period of analysis? It gives me just for 2500 (ps) in spite of the fact that I chose for 50(ns) or 5000(ps).
Thanks again
Dear Mohammad Rezayani
Honestly I have no idea. I doubt that is a GROMACS error, you would have seen some complaining on the screen.
Just a thing: 50 ns = 50000 ps. So basically your plot covers the time 0-25ns. Are you sure that your simulation is 50ns long? Or that when you compute the values the terminal isn't complaining about something in any way? Because if you ask for 50k ps and it print the first 25k, it should be telling you if an error occurs or if your trajectory is smaller than the requested time period.
Dear Nicola Piasentin
Thank you again for your help.
You are right. it was just a writing error.
I am sure my simulation time is 50 ns. I must double check to get the problem.
Thanks again
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