[gmx-users] Number Density

[Dr. Vitaly Chaban]

I would guess that the density is zero at the center, since you do not have
solvent molecules inside the membrane.

Yes, the output density is number of interaction sites per nm^3, calculated
in each slice, whose size you had specified.


Dr. Vitaly V. Chaban


On Sun, Sep 15, 2013 at 5:23 PM, Sun Moon <sunmoon1360 at yahoo.com> wrote:

> 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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