Hello: I am attempting to use the gmx density function to calculate the electron density of a bilayer system with and without a solute. In order to do this, I must calculate the density of various elements (i.e., lipid head groups, lipid tails, solvent molecules) along the bilayer normal (z axis) for both a pure bilayer system that I have run and a similar one containing the solute, and then I must find the difference between the respective electron density profiles. However, each system has slightly different box z-dimensions, so the two instances of running the gmx density command result in differently spaced intervals along the axis. This makes it hard to compute the difference.
Is there a specification by which I can choose the starting and ending place along the z-axis for my density calculation, such that I can have even intervals spaced at the same places for both of my calculations? I have tried changing the number of slices to approximately accommodate for the differences, but it still isn't working. Any help would be appreciated. Thanks! Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
