[gmx-users] About densmap tool

Yasser Almeida Hernández yasser.almeida.hernandez at chemie.uni-hamburg.de
Wed May 8 16:48:48 CEST 2019


I am working with a membrane protein inserted in a heterogeneous 
bilayer, with different lipids at different ratios. I used gmx densmap 
to obtain 2D maps of the lipids distribution, based in the PO4 group. I 
use the command as following:

gmx densmap -s <str_file.gro> -f <traj_file.xtc> -n <index_file.ndx> -od 
<densmap_lipid_X.dat> -unit nm-2 -bin 0.1

Attached is one example of one of my raw output maps.

According with the command-line reference: "The normalization of the 
output is set with the -unit option. The default produces a true number 
density. Unit nm-2 leaves out the normalization for the averaging or the 
angular direction. Option count produces the count for each grid cell. 
When you do not want the scale in the output to go from zero to the 
maximum density, you can set the maximum with the option -dmax."

I am not sure if I am interpreting the results in a proper way.

1 - If "Unit nm-2 leaves out the normalization for the averaging or the 
angular direction", what do the numbers in the output file actually mean?

2 - Are they the average in each grid point, along the whole simulation 

3 - It may sound as a silly question, but how does this command define 

Thanks in advance


Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
+49 40 42838 2845
yasser.almeida.hernandez at chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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