Hi, everyone:
I have used Amber 9 to carry out 3 ns molecular dynamics simulation for one cyclo-peptide molcule in water phase to study the conformation variation of peptide. In order to find different low energy conformation, RMSD values for 3000 conformation extracted from MD trajectory are calculated (the initial conformation as the reference). Then RMSD values versus time is plotted. It is found that RMSD has a large fluctuation between 0 to 1 for cyclo-tetra-peptide and cannot reach the equilibrium. But this phenomena is not found for cyclo-tri-peptide and cyclo-penta-peptide which RMSD fluctuation is more stable. And extend the simulation time has no help to solve the problem.The same settings of MD simulations are applied for these systems. Now, I have not found the solution to this problem. Anyone can give me some suggestions. Thank you for your great help.
Min Chiju
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Received on Mon Apr 23 2012 - 04:30:03 PDT
