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 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
Hi,
Length of the ACF, as default, is half the number of frames and indeed your graph show a length of 25000 ps
The graph report the ACF for the three components of the moment of inertia.
To calculate ACF of Rg you can use other tools. gmx analyze can also do that
https://manual.gromacs.org/current/onlinehelp/gmx-analyze.html
Best regards
Alessandra
Dear Alessandra
Thank you very much for your constant help.
Dear Alessandar
I fixed the problem but some part of radius of gyration ACF is under zero! How can I interpret it? What happens to polymer radius of gyration showing such behavior in ACF?
Thanks
Dear mj.rezayani,
Could you please tell me what is the usage of ACF of radius of gyration?
I have seen your question recently and It is interesting to me to know more about ACF of Rg.
I apperciate your responses.
Best
Dear MOH4,
We usually can use ACF of different parameters like Rg to check if our system is equilibrated or no, especially in case of polymers. Assume, your polymer chain is not relaxed, it is streched(at first of simulation) and must be in random coil. ACF shows that polymer chain is going to equilibrated state with time and after a specific time ACF reached to zero and fluctuate around it. fluctuation around zero means your system is equilibrated and we can find minimum required time for simulation. For example, at 20 ns the plot of ACf reaches to zero, then minimum time required for simulation is 20 ns.
Best,
Mohammad
