Dear users,
To calculate "Number Density" of solvent via size box for a bilayer membrane, I
used g_density
program as the following:
g_density -f md.xtc -s md.tpr -o density-Num-SOL.xvg -d z
-dens number -n index-group.ndx
I got
@ title
"Partial densities"
@ xaxis label "Box (nm)"
@ yaxis label "Number density (nm\S-3\N)"
0 96.8219
0.131123 96.1793
0.262246 95.33
0.393369 93.1889
0.524492 89.4451
0.655615 82.8209
0.786738 73.8842
0.917861 63.6742
1.04898 52.7296
1.18011 42.8748
1.31123 33.0874
1.44235 23.2632
1.57348 13.9631
1.7046 7.12264
1.83572 2.95836
1.96684 1.03366
2.09797 0.293438
2.22909 0.0784924
2.36021 0.0134454
2.49134 0.00272543
2.62246 0.00254373
2.75358 0.00872137
2.8847 0.0168977
3.01583 0.0168977
3.14695 0.00853968
3.27807 0.0143539
3.4092 0.0230753
3.54032 0.0121736
3.67144 0.00345221
3.80257 0.00908476
3.93369 0.0403363
4.06481 0.203317
4.19593 0.806
4.32706 2.62005
4.45818 6.88243
4.5893 13.8779
4.72043 22.6425
4.85155 32.1406
4.98267 41.1066
5.11379 50.7564
5.24492 60.6579
5.37604 71.2691
5.50716 80.5771
5.63829 87.9612
5.76941 93.1096
5.90053 95.5782
6.03165 96.5369
6.16278 96.4884
6.2939 96.6515
6.42502 96.3772
What is the concept number density with gromacs? Is it especial
volume (nm-3)? If so, why does in the central of box this amount is
zero?
What is N in “(nm\S-3\N)” dimension for number density?
Thanks in advance,
SUN
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