Dear all, Any idea on my questions, please? Mostafa; Using gmx densmap first produce a .xpm file; ~> gmx densmap -f case.xtc -s case.tpr -n index.ndx -o case.xpm -unit nm-3 -bin 0.02 The case.xpm file is a matrix, one way provided by Gromacs to visualize a matrix is to convert it to a eps file for instance, you can do that using gmx xmp2ps; ~> gmx xpm2ps -f case.xpm -di m2p.m2p -o case.eps -bx 2 -by 2 -rainbow blue
Thank you Alex On Tue, Feb 12, 2019 at 2:19 PM Mostafa Fakhraee < fakhraee.mosta...@gmail.com> wrote: > Dear Alex > > Is it possible to send the command you have used for extracting 2D densmap? > > > > On Tue, Feb 12, 2019 at 10:39 PM Alex <alexanderwie...@gmail.com> wrote: > > > Dear all, > > Following my last email, I also calculated the 2D density number for > water > > molecules for the same system, as you can see in the link below the > maximum > > water number density interestingly is 120 nm^-3 for the region with the > > bulk water whose the number density should be around 33.36 nm^-3. The box > > size of my system is ``7.552, 7.552, 7.552" and the bin grid size was > > chosen to be 0.01 nm. > > I tried to make a connection between the 120 nm^-3 given for the bulk > water > > region by the gmx densmap and reall water number density of 33.36 nm^-3 . > > Considering the above box information I would be so appreciated if one > > could explain what I am doing wrong? > > > > https://drive.google.com/open?id=1HvSnUahNklTONmthYPXdCwB8g2kzRXVe > > > > Thank you > > Alex > > > > ---------- Forwarded message --------- > > From: Alex <alexanderwie...@gmail.com> > > Date: Tue, Feb 12, 2019 at 5:20 AM > > Subject: Maximum number density in gmx densmap > > To: gmx-us...@gromacs.org <gmx-us...@gromacs.org> > > > > > > Dear all, > > Using the gmx densmap I have calculated the 2D density number in x-y > plain > > for a droplet containing 58 molecules. With nm^-3 (nm^-2) as unit the > > maximum number density turn out to be 97.83 (738.38). I wonder what > exactly > > has been counted here as the representative of each molecules? Is it for > > instance the center of mass of each molecule? > > And is the gmx densmap exactly the gmx density but in two dimensions? > > > > Thank you, > > Regards > > 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 gmx-users-requ...@gromacs.org. > > > > > -- > ---- > Best Regards, > Mostafa Fakhraee > =================================== > PhD Student of Physical Chemistry, > Department of Chemistry, > Sharif University of Technology, Tehran, Iran. > Official Email: mostafa_fakhr...@ch.sharif.ir <mostafa.fakhr...@yahoo.com > > > Email: mostafa.fakhr...@yahoo.com > =================================== > -- > 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. > -- 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.