# Shell solvation density

**URL:** <https://gromacs.bioexcel.eu/t/shell-solvation-density/1876>\
**Category:** User discussions\
**Created:** [April 1, 2021, 12:48pm UTC](https://gromacs.bioexcel.eu/t/shell-solvation-density/1876 "2021-04-01T12:48:21Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![yasser.almeida](https://avatars.discourse-cdn.com/v4/letter/y/76d3ee/32.png) [@yasser.almeida](https://gromacs.bioexcel.eu/u/yasser.almeida)\
**Post date:** [April 1, 2021, 12:48pm UTC](https://gromacs.bioexcel.eu/t/shell-solvation-density/1876/1 "2021-04-01T12:48:21Z")

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GROMACS version:  
GROMACS modification: No

Hi,

I have a simple/general/dumb question, for clarification. I want to create a solvation shell around a solute at the standard water density, in a big box, that I will fill later with a different solvent.

If I run:  
`gmx solvate -cp solute.pdb -cs ../TIP3P_eq_box_6x6x6.gro -o solute_TIP3P_box.gro -p test.top -box 10 10 10`

… the output is:

```
Output configuration contains 100518 atoms in 33506 residues
Volume : 1000 (nm^3)
Density : 1002.34 (g/l)
Number of solvent molecules: 33505

```

So, the whole box is at 1 g/l. Now, if I run:  
`gmx solvate -cp solute.pdb -cs ../TIP3P_eq_box_6x6x6.gro -o solute_TIP3P_shell.gro -p test_shell.top -shell 1 -box 10 10 10`

…the output is:

```
Output configuration contains 540 atoms in 180 residues
Volume : 1000 (nm^3)
Density : 5.38472 (g/l)
Number of solvent molecules: 179

```

The density is higher, so I guess that the number is calculated with respect to the shell volume, not the box volume, right? (In order to get the solvation shell at 1 g/l I have to decrease the number of TIP3P waters with the `-maxsol` option.)

Thanks in advance.

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<div class="post-metadata">

**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [April 6, 2021, 12:08pm UTC](https://gromacs.bioexcel.eu/t/shell-solvation-density/1876/2 "2021-04-06T12:08:16Z")

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No, the density is nearly a factor 200 lower in the latter case. The density is always computed with respect to the box volume

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<div class="post-metadata">

**Author:** ![yasser.almeida](https://avatars.discourse-cdn.com/v4/letter/y/76d3ee/32.png) [@yasser.almeida](https://gromacs.bioexcel.eu/u/yasser.almeida)\
**Post date:** [April 6, 2021, 12:46pm UTC](https://gromacs.bioexcel.eu/t/shell-solvation-density/1876/3 "2021-04-06T12:46:42Z")

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Thank you for the reply.

> [@hess](#):
>
> No, the density is nearly a factor 200 lower in the latter case.

Which later case do you mean? When I use the `-shell` option or if I use the `-maxsol` option to decrease the number of TIP3P molecules? With `-shell` I get a higher density with less particles, that’s why I was wondering which volume was used for that calculation.

> [@hess](#):
>
> The density is always computed with respect to the box volume

So, the `-shell` option, in general, will produce over-dense systems?

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<div class="post-metadata">

**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [April 6, 2021, 1:30pm UTC](https://gromacs.bioexcel.eu/t/shell-solvation-density/1876/4 "2021-04-06T13:30:02Z")

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I don’t see any results with -maxsol in your post. With -shell the density is nearly a factor 200 lower.

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<div class="post-metadata">

**Author:** ![yasser.almeida](https://avatars.discourse-cdn.com/v4/letter/y/76d3ee/32.png) [@yasser.almeida](https://gromacs.bioexcel.eu/u/yasser.almeida)\
**Post date:** [April 6, 2021, 1:49pm UTC](https://gromacs.bioexcel.eu/t/shell-solvation-density/1876/5 "2021-04-06T13:49:48Z")

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This is what I get with the `-maxsol` option:

```
gmx solvate -cp solute.pdb -cs ../TIP3P_eq_box_6x6x6.gro -o solute_TIP3P_shell.gro -p test_shell.top -shell 1 -box 10 10 10 -maxsol 34

Output configuration contains 105 atoms in 35 residues
Volume : 1000 (nm^3)
Density : 1.04703 (g/l)
Number of solvent molecules: 34
```

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<div class="post-metadata">

**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [April 6, 2021, 2:04pm UTC](https://gromacs.bioexcel.eu/t/shell-solvation-density/1876/6 "2021-04-06T14:04:53Z")

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But have you now seen that the density is a factor 200 lower with -shell and even lower with -maxsol?

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<div class="post-metadata">

**Author:** ![yasser.almeida](https://avatars.discourse-cdn.com/v4/letter/y/76d3ee/32.png) [@yasser.almeida](https://gromacs.bioexcel.eu/u/yasser.almeida)\
**Post date:** [April 6, 2021, 2:16pm UTC](https://gromacs.bioexcel.eu/t/shell-solvation-density/1876/7 "2021-04-06T14:16:16Z")

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Oh sorry! I didn’t realize the decimal point in the first case, which gives basically kg/L.  
Of course, with `-shell` the density is lower.

Thanks