![]() ![]() ![]() It is necessary that the protein model and the chosen environment for the simulations should mimic the native environment as close as possible. Keywords: Molecular dynamics simulations, Conformational studies, Gromacs, Structural studies, Protein dynamics Background While molecular dynamics (MD) simulations are increasingly getting popular in studying protein dynamics in silico, there is a strong need to correlate the results with experimental observations. ![]() In this protocol, we provide a general approach and standard setup protocol for MD simulations by using the Gromacs MD suite. Abstract Molecular dynamics (MD) simulations have become one of the most important tools in understanding the behavior of bio-molecules on nanosecond to microsecond time scales. ![]()
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