<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hi,</div><div> I would like to know if there is a way in gromacs to calculate the time-averaged density of solvent which is confined between two objects , say, two plates or another example will be water confined between ligand and binding-pocket.</div><div>I was thinking about two ways for going about this but in both cases there are some issues:</div><div>1. I found there is a tool g_densmap but it gives a 2D density map. But, in this case, I guess, 3D map would have been necessary.</div><div><br></div><div> 2. Also, I found trjorder with -nshell option can calculate number of waters within a distance (with -r option) . But, in this case, I need to know volume of the confined space as well. I am not sure gromacs can calculate the volume of the confined space.</div><div><br></div><div>Any help or suggestion of
any other suitable methods will be highly appreciated.</div><div><br></div><div>Sanku</div><div><br></div></div></body></html>