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I have a 10 ns simulation and have removed the pbc and have used the nojump option so water can diffuse out. I wanted to calculate what are the remaining number of water molecules inside the box and what is the density at each step. I have used the gmx density function but my density is coming arround 997 at each time step
The -pbc options of ´gmx trjconv` do not remove the periodic boundary conditions. All water molecules are still in the box. It’s just a matter of representing them outside or inside the box.
how can i remove the periodic boundary conditions ?
First, what is it you are interested in? During the simulation all waters are inside the box all the time - that’s the meaning of a periodic box.
If you really want to calculate the density of an arbitrary number of water molecules (since during the simulations they are all interacting as if the unit cell was repeated infinitely) in an arbitrary volume (arbitrary in the way that it is not connected to the simulation that you ran) I’m afraid you’ll have to write a Python script (or something) to analyse the density of the water molecules that are within the coordinates that you want to consider (after -pbc nojump, so that the water molecules that have crossed the periodic boundary diffuse out of the unit cell).
Thank you for your guidance