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I have done md simulation of dna ligand complex for 300ns in which i got the rmsd of alone dna stable at 0.4 nm and that of complex at 1.5 nm . is there is any possibility of this increase in rmsd of complex. please suggest.
Hi,
Did you visualize the trajectory to check if no jump occur in the trajectory? In case you see the ligand jump in and out of the box. Maybe you want to run trjconv to remove this effect and recalculate the rmsd.
Best regards
Alessandra
Thank you for your help, as the ligand is present inside the box in the whole run. Please, can you explain how to run trjconv to remove this effect.
Thank you in advance.