Dear researcher,
I did a protein ligand Molecular Dynamic simulation and protein MDS for 50 ns both. In the Protein simulation, the RMSD is stable till 50ns. But when i add the ligand and simulate same protein was stable till 15ns and after that it shows abrupt pattern of RMSD (Fig attached). Is this protein really unstable or it is the problem with the MDS parameters? I did the simulation using GROMACS 4.5.6.
Please provide the probable reason for this kind of results.
Thanks in advance.
This is simply due to periodic boundary conditions. Remove jumps and make molecules whole before doing analysis like RMSD.
This is simply due to periodic boundary conditions. Remove jumps and make molecules whole before doing analysis like RMSD.
The RMSD "jumps" that you see are artifacts due to periodic boundary conditions
Before to run any analysis you have to sample your trajectories in order to remove PBC artifacts. You can do this by typing a command like "trjconv -pbc nojump ...".
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