[gmx-users] Fwd: Maximum number density in gmx densmap
alexanderwien2k at gmail.com
Wed Feb 13 17:23:19 CET 2019
Any idea on my questions, please?
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
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 xpm2ps -f case.xpm -di m2p.m2p -o case.eps -bx 2 -by 2 -rainbow blue
On Tue, Feb 12, 2019 at 2:19 PM Mostafa Fakhraee <
fakhraee.mostafa1 at 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 <alexanderwien2k at gmail.com> wrote:
> > Dear all,
> > Following my last email, I also calculated the 2D density number for
> > molecules for the same system, as you can see in the link below the
> > 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
> > 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 <alexanderwien2k at gmail.com>
> > Date: Tue, Feb 12, 2019 at 5:20 AM
> > Subject: Maximum number density in gmx densmap
> > To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> > Dear all,
> > Using the gmx densmap I have calculated the 2D density number in x-y
> > 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
> > 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
> > --
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> Best Regards,
> Mostafa Fakhraee
> PhD Student of Physical Chemistry,
> Department of Chemistry,
> Sharif University of Technology, Tehran, Iran.
> Official Email: mostafa_fakhraee at ch.sharif.ir <mostafa.fakhraee at yahoo.com
> Email: mostafa.fakhraee at yahoo.com
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