Dear Amber Community,
I am using a protein which is a homodimer. Since I am new to simulation, in the initial simulations, I had not given the nscm commend in the input file. Therefore, one of the chain of the dimer has gone outside the periodic box in half of the frames in the trajectory. In such scenario, mirror image of the chain comes in the simulation box which is away from its another bound chain. It gives a impression that there are 2 molecules simulating far apart in different corners of the simulation box.
When I performed RMSD analysis of the trajectory, It is giving weird graphs where RMSD shoots to very high value when one of the chain of dimer goes out of the box. Please suggest how can I solve this problem and align the protein properly for the simulation.
Thank You.
Regards,
Saurabh Shukla,
Graduate Research Assistant,
Department of Chemical and Biomolecular Engineering,
University of Illinois at Urbana Champaign, IL
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Received on Sun Apr 19 2015 - 18:30:02 PDT
