# Drastic change in number of Water Molecules after Point Mutation **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools\ **Created:** [June 26, 2023, 4:34am UTC](https://gromacs.bioexcel.eu/t/drastic-change-in-number-of-water-molecules-after-point-mutation/6684 "2023-06-26T04:34:22Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [June 26, 2023, 4:34am UTC](https://gromacs.bioexcel.eu/t/drastic-change-in-number-of-water-molecules-after-point-mutation/6684/1 "2023-06-26T04:34:22Z")
GROMACS version:2022.2 GROMACS modification: Yes/No Hi @jalemkul @hess @pjohansson upon mutating 1 residue in the receptor (` **protein-protein system** `), the number of added water molecules have been changed drastically. (Provided all parameters are same ie box size, force field, sol type, mdp parameters, simulation time etc…) mut\_1 =\> wild\_type to E484K → total SOL =\> 47997 mut\_2 =\> wild\_type to N501Y → total SOL =\> 76428 I am not sure if the number of water molecules affects the **`mdrun`** performance but this made my system very slow almost by 0.5. For mut\_1 and mut\_2, it took 72 Hrs and 140 Hrs respectively to finish the MD simulation. Two question: 1st: Is it obvious/known phenomenon of Gromacs to change the number of water molecules abruptly upon mutation? 2nd: Does the increased number of water molecules (SOL) makes the simulation slow as happned in my case? Thanks ---
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [June 28, 2023, 5:47am UTC](https://gromacs.bioexcel.eu/t/drastic-change-in-number-of-water-molecules-after-point-mutation/6684/2 "2023-06-28T05:47:11Z")
@jalemkul Please consider my query. ---
**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:** [June 28, 2023, 6:09am UTC](https://gromacs.bioexcel.eu/t/drastic-change-in-number-of-water-molecules-after-point-mutation/6684/3 "2023-06-28T06:09:10Z")
A single point mutation would not result in such a drastic change. Your box size must be different. ---
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [June 28, 2023, 6:43am UTC](https://gromacs.bioexcel.eu/t/drastic-change-in-number-of-water-molecules-after-point-mutation/6684/4 "2023-06-28T06:43:05Z")
Thanks for considering. I used the same script to generate topology. Don’t know what went wrong. I used the below command in the script to determine the box. “gmx editconf -f test.gro -o test\_newbox.gro -c -d 1.2 -bt triclinic -box 1.2 1.2 1.2” also, Does the number of water molecule affects the simulation speed i.e. time to finish the simulation? Thanks ---
**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:** [June 28, 2023, 6:58am UTC](https://gromacs.bioexcel.eu/t/drastic-change-in-number-of-water-molecules-after-point-mutation/6684/5 "2023-06-28T06:58:09Z")
Check the box vectors in any coordinate file to check your work. But there’s no physical way that 30,000 more waters will fit in a box that was otherwise filled with a smaller number of waters. The number of atoms in the system is principal determining factor in the speed of a simulation. More atoms means slower simulation (assuming everything else to be constant in terms of input settings and hardware). ---
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [June 28, 2023, 8:12am UTC](https://gromacs.bioexcel.eu/t/drastic-change-in-number-of-water-molecules-after-point-mutation/6684/6 "2023-06-28T08:12:24Z")
> [@jalemkul](#): > > The number of atoms in the system is principal determining factor in the speed of a simulation. It means, number of Solvent molecules doesn’t affect the simulation speed, so there is something wrong with Gromacs may be it has crashed or having some trouble. Thanks ---
**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:** [June 28, 2023, 8:27am UTC](https://gromacs.bioexcel.eu/t/drastic-change-in-number-of-water-molecules-after-point-mutation/6684/7 "2023-06-28T08:27:42Z")
No. More solvent molecules = more atoms. Your second simulation is slower because it has far more atoms than the first. ---
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [June 29, 2023, 12:41am UTC](https://gromacs.bioexcel.eu/t/drastic-change-in-number-of-water-molecules-after-point-mutation/6684/8 "2023-06-29T00:41:59Z")
Thanks :)