I have a protein containg 2138 amino acids in each chains. then i added POPC membrane and then add solvent ater and counter kcl ions..then i had done 025ns run for eqilibration by restrating protein, then again protein and lipid eqilibration with harmonic restraints run for 0.25ns then again whole system run for 0.25ns then finally done whole production run for 0.25 ns. after that when i performed RMSD calculation for whole system then i will constantly increasing. what will be the reason?
Your system either has yet to reach an energy minimized state, or the system adopts multiple conformation and is in equilibrium. I suspect that it has yet to reach a minimized state given the size of your protein. Does the RMSD continue to rise in a linear fashion? Or, are there discrete steps? Is your force field optimized for your in silico question?
If you plot RMSF per residue are you finding that domains, or subdomains of the system are moving together? I have worked with much smaller systems without membrane that needed microsec of dynamics simulation before I realized there are discrete conformations in equilibrium. You might gain some insight through lower resolution course-grained simulation such as elastic network modeling or, my favorite, anisotropic network modeling. These experiments take seconds to minute to calculate and are certainly worth the time.
0.25 ns is a very small time scale to see if the system is converging to equilibrium or not. Please increase the time to see if the RMSD converges or not.
Thanks Rohan, but can you say how much time frequency is minimum required for this?
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