[gmx-users] Fwd: Maximum number density in gmx densmap

Mostafa Fakhraee fakhraee.mostafa1 at gmail.com
Tue Feb 12 20:18:40 CET 2019

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 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 <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 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
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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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