# Some water molecules are missing **URL:** \ **Category:** User discussions\ **Created:** [November 1, 2023, 2:11am UTC](https://gromacs.bioexcel.eu/t/some-water-molecules-are-missing/7522 "2023-11-01T02:11:37Z")\ **Posts on this page:** 11\ **Page:** 1
**Author:** ![ok1](https://avatars.discourse-cdn.com/v4/letter/o/9d8465/32.png) [@ok1](https://gromacs.bioexcel.eu/u/ok1)\ **Post date:** [November 1, 2023, 2:11am UTC](https://gromacs.bioexcel.eu/t/some-water-molecules-are-missing/7522/1 "2023-11-01T02:11:37Z")
Hello, I would like to ask why after adding water solvent, the middle will appear in some places blank. Why aren’t these water molecules here?And what can I do to replace these missing water molecules? Or is there any code that just fills the bottom half of the box with water? Thank you ![8F}XK73(4UG$296T($O6N](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/4/41c3af9317db3c8bb4f3ce39103ba622c26cd5ed.png) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 1, 2023, 2:35am UTC](https://gromacs.bioexcel.eu/t/some-water-molecules-are-missing/7522/2 "2023-11-01T02:35:11Z")
Please provide the exact sequence of commands you have given. What you’re showing is very unusual. ---
**Author:** ![ok1](https://avatars.discourse-cdn.com/v4/letter/o/9d8465/32.png) [@ok1](https://gromacs.bioexcel.eu/u/ok1)\ **Post date:** [November 1, 2023, 3:19am UTC](https://gromacs.bioexcel.eu/t/some-water-molecules-are-missing/7522/3 "2023-11-01T03:19:03Z")
the code is “gmx solvate -cp em-vac.gro -cs spc216.gro -p fws.top -o fws-b4ion.gro -box 4 4 2” em-vac.gro is the ozone molecule . ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 1, 2023, 3:59am UTC](https://gromacs.bioexcel.eu/t/some-water-molecules-are-missing/7522/4 "2023-11-01T03:59:00Z")
It seems to me that the ozone coordinates are not centered in the specified box, so they are, in fact, there but they appear to be “outside” the box. If rewrapped, you are probably getting the ozone/water layer that you expect. Normally one centers a solute within a given unit cell and then adds solvent after the fact. ---
**Author:** ![ok1](https://avatars.discourse-cdn.com/v4/letter/o/9d8465/32.png) [@ok1](https://gromacs.bioexcel.eu/u/ok1)\ **Post date:** [November 1, 2023, 7:29am UTC](https://gromacs.bioexcel.eu/t/some-water-molecules-are-missing/7522/5 "2023-11-01T07:29:58Z")
But I added the water solution after I created the box with the code“ gmx editconf -f fws.gro -o fws-PBC.gro -bt cubic -box 4 4 4 ” and put the ozone molecule in the center. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 1, 2023, 1:36pm UTC](https://gromacs.bioexcel.eu/t/some-water-molecules-are-missing/7522/6 "2023-11-01T13:36:19Z")
And then you are telling `gmx solvate` to use a different box with `-box 4 4 2`. If you want to create a layered system, there is an approach discussed here: [Building Biphasic Systems](http://www.mdtutorials.com/gmx/biphasic/index.html) ---
**Author:** ![ok1](https://avatars.discourse-cdn.com/v4/letter/o/9d8465/32.png) [@ok1](https://gromacs.bioexcel.eu/u/ok1)\ **Post date:** [November 3, 2023, 7:43am UTC](https://gromacs.bioexcel.eu/t/some-water-molecules-are-missing/7522/7 "2023-11-03T07:43:17Z")
In fact, I just want to fill the bottom half of the box with water molecules with ozone, is that creating a layered system? If not, then what should I do. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 3, 2023, 9:40am UTC](https://gromacs.bioexcel.eu/t/some-water-molecules-are-missing/7522/8 "2023-11-03T09:40:08Z")
I don’t understand your question. Can you diagram out what you’re trying to accomplish? ---
**Author:** ![ok1](https://avatars.discourse-cdn.com/v4/letter/o/9d8465/32.png) [@ok1](https://gromacs.bioexcel.eu/u/ok1)\ **Post date:** [November 3, 2023, 1:03pm UTC](https://gromacs.bioexcel.eu/t/some-water-molecules-are-missing/7522/9 "2023-11-03T13:03:47Z")
I wanted to implement this model ![(XLPH@E3)O3IFQ1(WN8K41E](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/6/6d45198cb7c7263c3ce015805d27a8b5ee91e0a3.png) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 3, 2023, 3:19pm UTC](https://gromacs.bioexcel.eu/t/some-water-molecules-are-missing/7522/10 "2023-11-03T15:19:49Z")
Then the approach is the same as in the tutorial. Build the initial box of ozone, position it in a new box that is doubled in size along one axis, and solvate the void space with water. If that leads to water being mixed with the ozone layer, then simply generate two boxes with the appropriate dimensions and concatenate them. ---
**Author:** ![ok1](https://avatars.discourse-cdn.com/v4/letter/o/9d8465/32.png) [@ok1](https://gromacs.bioexcel.eu/u/ok1)\ **Post date:** [November 6, 2023, 12:20pm UTC](https://gromacs.bioexcel.eu/t/some-water-molecules-are-missing/7522/11 "2023-11-06T12:20:39Z")
Excuse me, I would like to ask how to connect the two boxes together. And I want to know if the initial ozone box was not completely filled with ozone molecules，at this point,whether making the box extended, and then using water solvent will cause the entire large box to be filled with water or not.