# Increasing carbon's van der Waals radius to delete water molecules **URL:** \ **Category:** User discussions\ **Created:** [July 19, 2020, 1:40pm UTC](https://gromacs.bioexcel.eu/t/increasing-carbons-van-der-waals-radius-to-delete-water-molecules/526 "2020-07-19T13:40:16Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\ **Post date:** [July 19, 2020, 1:40pm UTC](https://gromacs.bioexcel.eu/t/increasing-carbons-van-der-waals-radius-to-delete-water-molecules/526/1 "2020-07-19T13:40:16Z")
hello. I used charmm-gui for building micelle-protein complex. I increased carbon radius for removing water inside the micelle. but nothing happend! Should I do something with charmm-gui to build a correct structure without water inside it? the following picture showes water density in the box, water density should be zero at the center of the micelle!! . ![dens_water_p](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/9f1d8197e946c49ef92bfbf180f0bf853e0f0c40.png) ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [July 19, 2020, 11:20pm UTC](https://gromacs.bioexcel.eu/t/increasing-carbons-van-der-waals-radius-to-delete-water-molecules/526/2 "2020-07-19T23:20:50Z")
You are best directing this question to those who provide the charmm-gui, this is not a GROMACS issue. ---
**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\ **Post date:** [July 19, 2020, 11:46pm UTC](https://gromacs.bioexcel.eu/t/increasing-carbons-van-der-waals-radius-to-delete-water-molecules/526/3 "2020-07-19T23:46:46Z")
I know it isn’t gromacs issue. But I thought maybe some body had the same problem who can help me now. Anyway, Thank you. ---
**Author:** ![kevinboyd](https://avatars.discourse-cdn.com/v4/letter/k/c77e96/32.png) [@kevinboyd](https://gromacs.bioexcel.eu/u/kevinboyd)\ **Post date:** [July 21, 2020, 2:16am UTC](https://gromacs.bioexcel.eu/t/increasing-carbons-van-der-waals-radius-to-delete-water-molecules/526/4 "2020-07-21T02:16:37Z")
Hi - depending on what you’re trying to study, if you just run the simulation for a while the water will eject eventually. You could restrain the micelle atoms in the meantime. ---
**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\ **Post date:** [July 21, 2020, 11:23am UTC](https://gromacs.bioexcel.eu/t/increasing-carbons-van-der-waals-radius-to-delete-water-molecules/526/5 "2020-07-21T11:23:41Z")
Thanks for your response. I ran the simulation for more 100 ps but water density increased at the center of the structure even though my structure seems more compact than before!! my first structure: ![first](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/b26ddfbc2447f4b318ac7c5dd8965ef1270682d7.jpeg) ![dens](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/bae2110fbba4755208f970997bd5b15a8364774e.png) after simulation: ![final](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/dbb2aa018cea074752b6adfcc3d273ebe131ed00.jpeg) ![dens-final](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/5e63f002d6716f61990cdc61962eeec2798227fa.png) ---
**Author:** ![kevinboyd](https://avatars.discourse-cdn.com/v4/letter/k/c77e96/32.png) [@kevinboyd](https://gromacs.bioexcel.eu/u/kevinboyd)\ **Post date:** [July 22, 2020, 1:00am UTC](https://gromacs.bioexcel.eu/t/increasing-carbons-van-der-waals-radius-to-delete-water-molecules/526/6 "2020-07-22T01:00:23Z")
You wouldn’t expect to see ejection on that timescale, more like 10s to 100s of nanoseconds. Also what is your coordinate/command for gmx density? ---
**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\ **Post date:** [July 22, 2020, 10:06am UTC](https://gromacs.bioexcel.eu/t/increasing-carbons-van-der-waals-radius-to-delete-water-molecules/526/7 "2020-07-22T10:06:29Z")
Thank you so much… So you think nothing is wrong with the initial structure and it’s just about timescale. This is my command: gmx density -s nvt.tpr -f nvt.xtc -o dens\_nvt.xvg -d Z ---
**Author:** ![kevinboyd](https://avatars.discourse-cdn.com/v4/letter/k/c77e96/32.png) [@kevinboyd](https://gromacs.bioexcel.eu/u/kevinboyd)\ **Post date:** [July 22, 2020, 3:30pm UTC](https://gromacs.bioexcel.eu/t/increasing-carbons-van-der-waals-radius-to-delete-water-molecules/526/8 "2020-07-22T15:30:13Z")
If you’re slicing along the z dimension, but your micelle doesn’t cover the entire box in that dimension (which it wouldn’t because it has finite size), gmx density is also picking up the waters in those z-slabs **outside** of the micelle. I think you’re just misinterpreting gmx density ---
**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\ **Post date:** [July 23, 2020, 8:09pm UTC](https://gromacs.bioexcel.eu/t/increasing-carbons-van-der-waals-radius-to-delete-water-molecules/526/9 "2020-07-23T20:09:09Z")
Thank you kevin. All bests for you:)