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Hello there,
I have few queries, first I have simulated a protein using simulated annealing from 300K to 500K. I want to obtain radius of gyration of this simulated annealing trajectory with reference to initial structure. can I do it ?? I simply want to be able distinguish whether my protein is completely disorder in compare to initial structure. I have tried dssp analysis using mdtraj library and my dssp plot didnt make any sense(still have secondary structure). Do you guys have any other way besides Rg to determine whether my protein is completely lost its native state.?? As well as if I can compare my Rg in reference to initial structure, that way I will be able to distinguish the state
you can calculate the radius of gyration via the function “gyrate”. As far as I understand it gyrate calculates the radius of gyration for each time step of your trajectory. So you could see how the radius of gyration changes with time.
Because I did not find information about wether gyrate considers periodic boundary conditions, I ran a test with rather large molecules (pentaerythritol tetraoctanoate):
I calculated the radius of gyration once from the PBC-uncorrected trajectory and once with a PBC-corrected trajectory (trjconv with the flag -pbc whole) and the results were identical.
So I would conclude that the program takes pbc into consideration by itself without the need to convert the trajectory, though a confirmation would be welcome.