The options about xmax and xmin for gmx densmap

User discussions
1

GROMACS version: 2023
GROMACS modification: No
Hi,
I have a uniform medium system in a periodic box of 6.01 nm × 6.01 nm × 6.01 nm. After running gmx densmap three times, here are the results.

The One:

Command line:
  gmx densmap -f pro.xtc -s pro.tpr -n bulk.ndx -od check1.dat -xmin 0 -xmax 2 -b 100000 -e 200000
...
Select a group: Selected 7: 'SPE'
Last frame      20000 time 200000.000   

  The maximum density is 31.993681 (nm^-3)

The Second:

Command line:
  gmx densmap -f pro.xtc -s pro.tpr -n bulk.ndx -od check1.dat -xmin 2 -xmax 4 -b 100000 -e 200000
...
Select a group: Selected 7: 'SPE'
Last frame      20000 time 200000.000   

  The maximum density is 32.243793 (nm^-3)

The Third:

gmx densmap -f pro.xtc -s pro.tpr -n bulk.ndx -od check1.dat -xmin 0 -xmax 4 -b 100000 -e 200000
...
Select a group: Selected 7: 'SPE'
Last frame      20000 time 200000.000   

  The maximum density is 62.486565 (nm^-3)

The number density results show that when the x-range (xmax - xmin) is 4, the value is twice that of when the x-range is 2. Why is this the case?

2

When you average over z=0 to 4 you get about double the density compared to the half-sized range z=2 to 4, assuming a homogeneous system.