# Curve in water MSD **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools\ **Created:** [January 10, 2025, 4:34pm UTC](https://gromacs.bioexcel.eu/t/curve-in-water-msd/10999 "2025-01-10T16:34:54Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![maham](https://avatars.discourse-cdn.com/v4/letter/m/c77e96/32.png) [@maham](https://gromacs.bioexcel.eu/u/maham)\ **Post date:** [January 10, 2025, 4:34pm UTC](https://gromacs.bioexcel.eu/t/curve-in-water-msd/10999/1 "2025-01-10T16:34:54Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I have performa 500 ps simulation of just the water molecules (SPC) model. Towards the end I can see a curve. I am unable to understand the reason behind it. can anyone explain ? ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/2/2cfe8ee303359777b9972715b98eab7a69ae5ee7.png) ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [January 11, 2025, 11:20pm UTC](https://gromacs.bioexcel.eu/t/curve-in-water-msd/10999/2 "2025-01-11T23:20:36Z")
I would say that 100 water molecules and 500ps are both a very limited number of molecules and a very short time. You should have a longer run with many more molecules, as I can’t even think about how can 100 molecules fit in a box without PBC artifacts. ---
**Author:** ![maham](https://avatars.discourse-cdn.com/v4/letter/m/c77e96/32.png) [@maham](https://gromacs.bioexcel.eu/u/maham)\ **Post date:** [January 12, 2025, 11:38am UTC](https://gromacs.bioexcel.eu/t/curve-in-water-msd/10999/3 "2025-01-12T11:38:39Z")
there were around 8000 water molecules in the box but i wanted to check the MSD of a few 100. ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [January 13, 2025, 9:34am UTC](https://gromacs.bioexcel.eu/t/curve-in-water-msd/10999/4 "2025-01-13T09:34:00Z")
Why? Does the kind stay there if you do the average over all the water molecules? ---
**Author:** ![maham](https://avatars.discourse-cdn.com/v4/letter/m/c77e96/32.png) [@maham](https://gromacs.bioexcel.eu/u/maham)\ **Post date:** [January 13, 2025, 12:03pm UTC](https://gromacs.bioexcel.eu/t/curve-in-water-msd/10999/5 "2025-01-13T12:03:06Z")
no, its a linear line when I average over all water molecules. ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [January 13, 2025, 1:04pm UTC](https://gromacs.bioexcel.eu/t/curve-in-water-msd/10999/6 "2025-01-13T13:04:48Z")
Then probably you have your answer: you need more statistics to get a better MSD estimate! :) I might be wrong, but also I think the associated error to your diffusivity from the MSD you plot is going to be small even with the kind. Nevertheless, the more statistics the better. ---
**Author:** ![cathrine](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cathrine/32/1736_2.png) [@cathrine](https://gromacs.bioexcel.eu/u/cathrine)\ **Post date:** [January 14, 2025, 4:20pm UTC](https://gromacs.bioexcel.eu/t/curve-in-water-msd/10999/7 "2025-01-14T16:20:28Z")
The MSD curves tend to be noisier as time increases since the variance in molecule displacement becomes higher (there is more time for molecule pathways to diverge in the chaotic system), so that’s why you get the noise at the end of the curve. As previously discussed in this post, including more water molecules in your average should get rid of the bump. Hope this answered your question! ---
**Author:** ![maham](https://avatars.discourse-cdn.com/v4/letter/m/c77e96/32.png) [@maham](https://gromacs.bioexcel.eu/u/maham)\ **Post date:** [January 14, 2025, 6:36pm UTC](https://gromacs.bioexcel.eu/t/curve-in-water-msd/10999/9 "2025-01-14T18:36:44Z")
Thank you so much ---
**Author:** ![maham](https://avatars.discourse-cdn.com/v4/letter/m/c77e96/32.png) [@maham](https://gromacs.bioexcel.eu/u/maham)\ **Post date:** [January 14, 2025, 6:37pm UTC](https://gromacs.bioexcel.eu/t/curve-in-water-msd/10999/10 "2025-01-14T18:37:13Z")
Thank you so much. I can better understand it now