again when we perform MD simulation of Drug-DNA complexes; we do Equilibrium MD Simulation. Can we perform Non-Equilibrium MD Simulation also or not for such systems? Also if we can, the what are the softwares and how our result is going to be effected? And if we don't, then why?
Non-Equilibrium MD simulation is feasible. It seems that it is possible using the MP-CAFEE method (Massively Parallel Computation of Absolute binding Free Energy). By ensemble simulation, binding affinity prediction is performed by obtaining the binding strength (binding free energy) of DNA and Drug accurately and robustly. Equilibration calculation is performed at five kinds of initial velocities at 50 ns and the calculated result is used to calculate nonequilibrium at 2 ns under 32 conditions at six initial velocities. Although it is the calculation result, in the docking simulation using the conventional MD, the prediction correct answer rate is about 5%, but if you use the MP-CAFEE method, it is possible that it may considerably rise to about 70% . This calculation needs to be done with the world's fastest super computor. However, it will be possible for general researchers to calculate after a few years.
thank you, yuji kohno sir, will study more on this and get back to you with further doubts..
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