Hi
Can these be considered as a converged system. It’s two different simulation for 2 different proteins not related. What’s the acceptable fluctuation (range of max and min) that still shows convergence? If it’s not converged how to I extend my simulation from 30 ns? If I extend it, will the data be added to the xtc file directly? Thank you.
There isn’t really any specific convention for how much fluctuation is acceptable, it all depends on the system being studied and what exactly you’re trying to investigate about the system. If you need to extend the simulation, you can follow Extend or continue a GROMACS simulation - Compchems under the ‘Extend a simulation’ section, and the section below that describes how to combine the resulting xtc files into one file
Does these RMSD calculations are after PBC correction?
Thank you @Karis.
@scinikhil yes I removed PBC using the following command:
gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -center
We dont know what you are doing, so it is hard to say anything. for extending simulation you can refer here: https://manual.gromacs.org/current/user-guide/managing-simulations.html
@scinikhil Thank you.
Hi please let me know if this can be considered acceptable if I use frames from 23-30 ns for analysis? Thank you.
Look like your molecule having a pbc issue, visualise the trajectories to see if there is a sudden jump or rotation/translation motion.
Hi thank you I will visualise and correct that.
