The molecular simulation of two 50 amino acid long helical proteins forming heterodimer has ran 100ns then again ran for 50 ns. But the RMSD graph deformed. I have used gromacs 5.0 and saved it nopbc.xtc format . The graph is attached below. Kindly help me!
i think you should draw your graphs using xmgrace or matlab then it will be more clear.
For me this looks most likely to be a wrapping problem. One or parts of the monomors jump between periodic images. Unwrap your trajectorye.g. with gmx trajconv with the -pbc nojump option. If this doesn't help, you probably have to play around with the unwrapping in order to keep the dimer assembled and whole.
did you correct for pbc? It looks like this is the problem. is your box big enough for the protein not to feel its periodic image?
I have used triclinical box and also used "trajconv no jump" option, but it didn't help me. Is there can be any mistake in the minimization process? Norman Geist
If you load the unwrapped trajectory to VMD and play across the frames, I'm confident that you will see jumps across the periodic boundaries. One trick that may help is to center one of the monomoers in the center of the cell and than use the nojump option again. It would also help to have a picture of the distorted system. You have to have your dimer whole in order to measure its RMSD.
Or you can use gmx trjconv with -pbc mol -center and then compute the rmsd
Thank you Ioana Mariuca Ilie and Norman Geist . I will try these options .
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