I have tried to do a 50ns of the GABA receptor (a tetrameric protein) with a ligand and after the simulation i noticed the different units of the GABA receptor moving about as i was playing the trajectory. I expected the four chains of the protein to stick together and maintain the quarternary structure of the protein during the simulation so i can observe the interaction of the ligand with the receptor. How can i prevent the receptor protein units from moving about independently during the simulation? I have attached the image of the visualization of the .gro file in VMD just before loading the .xtc file. Would be glad to get help from anyone who can give me a way out. Thanks
See if removing pbc help. You can try gmx trjconv command for centering the protein.
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