I had ran molecular dynamic simulation on apo protein using TIP3P, TIP4P, TIP4PEW and SPC for 25 ns to establish the most suitable solvent model for specific protein. However, none of them gave low RMSD value. The lowest RMSD value is between 3.0 - 3.5 for TIP3P. But when I ran the protein with the ligand, the RMSD value become higher around 3-4. So what other parameter that I need to consider to establish the model?
Hi..
Read the attached article... May be you will get an idea related to you problem..
Article Comparison of various implicit solvent models in molecular d...
It should also depend on how you handle with best-fitting and whether backbone, heavy atoms or all atoms are used in the RMSD calculation.
It also depends on which forcefield you used. For example, AMBER15ipq is optimized with SPC/e-b while CHARM36 takes advantage of TIP3P. Be sure that you used the suitable models and parameters for corresponding force field.
So you start from a crystal structure and also using this for the RMSD? Have you carefully heated up the system? Are you sure your temperature was at reasonable levels at all time. What FF are you using for the Protein.
I do have concerns that the reason for the high RMSD is related to the solvent model. Can we have a PDB?
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