# Solvating without having water molecule "inside" the solute

**URL:** <https://gromacs.bioexcel.eu/t/solvating-without-having-water-molecule-inside-the-solute/5820>\
**Category:** User discussions\
**Created:** [February 17, 2023, 4:24am UTC](https://gromacs.bioexcel.eu/t/solvating-without-having-water-molecule-inside-the-solute/5820 "2023-02-17T04:24:35Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![zijiewu](https://avatars.discourse-cdn.com/v4/letter/z/9d8465/32.png) [@zijiewu](https://gromacs.bioexcel.eu/u/zijiewu)\
**Post date:** [February 17, 2023, 4:24am UTC](https://gromacs.bioexcel.eu/t/solvating-without-having-water-molecule-inside-the-solute/5820/1 "2023-02-17T04:24:35Z")

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GROMACS version:  
GROMACS modification: No

I am trying to solvate a bunch of cellulose chains with waters using `gmx solvate`. but it seems that no matter what I do, there will be water molecules (shown in yellow) “in between” the cellulose chains (shown in cyan) since the chains are sufficiently far away from each other. Is there a good way for me to force the solvation to happen only “outside” of the entire packed cellulose structure (outside the outmost cellulose chains)?

Or equivalently, is there a way for me to specify a minimum distance between solute and solvent during solvation without messing up the water density (meaning not using `gmx solvate -scale`)? If so, I can simply define a larger value for this minimum distance.  
 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/f/f26d3d3d80120716d7dfd123b81a3a902f20e436.jpeg)  
Thanks in advance!

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**Author:** ![MichelePellegrino](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/michelepellegrino/32/628_2.png) [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\
**Post date:** [February 17, 2023, 10:00am UTC](https://gromacs.bioexcel.eu/t/solvating-without-having-water-molecule-inside-the-solute/5820/2 "2023-02-17T10:00:08Z")

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Hi, have you tried changing `-radius`?

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<div class="post-metadata">

**Author:** ![zijiewu](https://avatars.discourse-cdn.com/v4/letter/z/9d8465/32.png) [@zijiewu](https://gromacs.bioexcel.eu/u/zijiewu)\
**Post date:** [February 17, 2023, 3:43pm UTC](https://gromacs.bioexcel.eu/t/solvating-without-having-water-molecule-inside-the-solute/5820/3 "2023-02-17T15:43:33Z")

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Hi Thanks! From GROMACS manual,

. A database (`vdwradii.dat` ) of van der Waals radii is read by the program, and the resulting radii scaled by `-scale` . If radii are not found in the database, those atoms are assigned the (pre-scaled) distance `-radius` .

This seems to suggest that -radius only has an effect when the vdW radii of the atom is not found in the database, but my atoms are just C, H, and O which are all in the database already. Did I misunderstand something over here?

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**Author:** ![MichelePellegrino](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/michelepellegrino/32/628_2.png) [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\
**Post date:** [February 17, 2023, 4:01pm UTC](https://gromacs.bioexcel.eu/t/solvating-without-having-water-molecule-inside-the-solute/5820/4 "2023-02-17T16:01:29Z")

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Ok… Then I guess you can remove water afterwards by doing a selection (`gmx select`) of cellulose + water outside the fibers.  
[https://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html](https://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html)