Hello Stéphane, I happened to use densmap and xpm these days for my ion channel.
Here is an example that you can play with for your system. gmx densmap -f md.xtc -s md.tpr -n index.ndx -aver z -bin 0.05 -dmin 0 -dmax 20 -unit nm-2 -o md.xpm ( later choose the group you are interested in) -aver z means we want to get top view, that is going to show your dense map in xy plane. -bin width, you can play with it to get best view. more options, you can check with densmap -h gmx xmp2ps -f md.xpm -o md.eps -rainbow blue eps file can be opened either by eps viewer or photoshop. Thanks, Best Wenjuan On Tue, Oct 23, 2018 at 7:49 AM ABEL Stephane <stephane.a...@cea.fr> wrote: > Dear all, > > I would like to obtain a 2D density map plot as for instance Fig. 4 in the > following paper (DOI 10.1007/s00232-014-9690-8) for a membrane protein > inserted in a surfactant micelle with gmx densmap and xpm2ps . I have few > questions > > - Have any of you ever done this type of plot? If yes, how? > - What parameters for densmap and/or xpm2ps did you use? > - How did you combine the protein and surfactant xpm files into a single > one to obtain the same plot as Fig. 4 > > Thanks in advance for your help > > Stéphane > -- > 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. > -- Best regards Wenjuan Jiang -- 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.