dear fellow researchers, I would like to ask if there any of you work with molecular dynamics for the protein-ligand complex. I attached the input generator script for namd obtained with Charmm-Gui force field. what is the meaning of "restartfreq" meaning? is there any thresehold of common value that we need to input for that part? the same question also applied for outputEnergies and outputTiming, is there any consideration to be concerned to decide how much value that we need to fill for restartfreq, outputEnergies and outputTiming
RestartFreq is a keyword that controls how often a restart file would be generated. This becomes particularly important if you are running a really long simulation, here you expect to restart from some intermediate confirmations/states. If you set it to too small a value, It would slow down your simulation due to significant I/O calls, but too large a value would make it difficult to control the generation of adequate start points.
thank you Hemanth Haridas for your response, is there any recommendation to calculate the value for restartFreq? For example I want to run for5 ns (just exercise) with 2 fs for every step, how much is restartFreq value that is considered proper for the simulation?
@Listiana No, it purely depends on what are you looking for, and how much space you have on the computer.
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