I used LAMMPS software for polymer nanocomposite system and the system is equilibrated for 10^7 MD steps with a δt = 0.001/0.002 and the data for postprocessing is collected every 10000 steps from subsequent production runs of an additional 10^6 MD steps.
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Dear Dr Gautum
"MD" typically refers to "Molecular Dynamics," a computational simulation method used to study the behavior of atoms and molecules over time. The amount of time required for a molecular dynamics simulation is highly dependent on several factors, including the complexity of the system being studied, the desired level of accuracy, the computational resources available, and the specific simulation parameters being used.
The time step used in a molecular dynamics simulation is usually in the range of femtoseconds (10^-15 seconds) to picoseconds (10^-12 seconds). This time step determines how often the simulation calculates the forces and updates the positions and velocities of the atoms in the system. The total simulation time is then a product of the number of time steps and the time step size.
For example, if you are simulating a system for 1 nanosecond (10^-9 seconds) with a time step of 1 femtosecond, you would need 1,000,000 time steps to cover that time span.
Keep in mind that the length of a simulation doesn't directly correlate with the accuracy of the results. Longer simulations can provide more statistically significant data, but the choice of simulation parameters and the quality of the force field used (if applicable) are also crucial factors in determining the reliability of the results.
Additionally, the computational resources available play a significant role in how quickly a simulation can be performed. More powerful hardware can complete simulations faster. Some simulations might take hours, while others could take days, weeks, or even longer.
In summary, there is no fixed answer to how many nanoseconds are required for a molecular dynamics simulation, as it depends on various factors. Scientists and researchers often perform preliminary tests to determine an appropriate simulation length based on their specific research goals and available resources.
Dear Gautam Bhardwaj,
In the MD simulation of protein ligand complex system, the fluctuation of root mean square deviation (rmsd) curve of molecules can be used as the convergence criteria.
Moreover, your aim of the MD simulation also play a role. Exploratory simulations might require less time, while detailed studies might need longer simulations.
I hope this will helps you.
Guanghao Qu