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

Alex alexanderwien2k at gmail.com
Tue Feb 12 20:09:12 CET 2019

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?


Thank you

---------- 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,

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