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GROMACS modification: Yes/No
Here post your question How can we run the total given time only for equilibrating the system not the production run?
Not sure how useful this late reply is going to be, but are you asking how to find how long the NPT equilibration ran for or are you asking how to get a .xtc file out of the equilibration step? If the former, that information is available in the npt.log file, and if the latter, you can add nstxout-compressed into npt.mdp as you would a regular md.mdp which should output a .xtc file for you
My question is the first one… In log file there is the time which I have given in mdp file… but I wanted to know that among that total time after a certain time density equilibriated. So that time after which density equilibriated should be the equilbriation time. But how I can understand that how much time will be needed for equilibriate the density.
As in the exact point at which the density reaches equilibrium? There isn’t really an exact criteria that comes with the program, most straightforward way would be to plot out the density against time (you can use ‘gmx energy -f npt.edr -o density.xvg’ and select 24 0) and see when the density begins to fluctuate around a relatively constant value