Dear users, I have simulated a protein dimer using OPLS-AA in 4.5.3 version. Analysing simulation showed that one of the monomer is out side the box. I tried trjconv pbc -nojump and trjconv -pbc mol still some fraction of a time one of them goes out. Can anyone suggest some solution to this. I need to calculate the radius of gyration of dimer, this value differs when i use treated and untreated trajectories. So Kindly suggest some solution.
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