Dear Users, I am trying to use the gmx spatial tool in order to understand how a solute interact with the protein. I performed the calculation following all the instructions (including the 2 trjconv steps). The trajectory obtained looks fine, and I calculated the sdf with the following command:
gmx_mpi spatial -f CALBtrjvonv2.xtc -s CALBMpr-1.tpr -n X.ndx and selecting the protein and an atom of my solute molecules (in the index) but when I open the grid.cube file with vmd and I visualize it as isosurface I have the density function even within the protein core... I thought that the density should be just around the protein (in this case). Moreover I have just positive values for the isosurface, is that normal? Am I doing something wrong? Thanks a lot, Valerio Ferrario -- 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 gmx-users-requ...@gromacs.org.