Drastic change in number of Water Molecules after Point Mutation

User discussions
1

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

2

@jalemkul Please consider my query.

3

A single point mutation would not result in such a drastic change. Your box size must be different.

4

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

5

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).

6

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

7

No. More solvent molecules = more atoms. Your second simulation is slower because it has far more atoms than the first.

8

Thanks :)