Problem about simulating the solution process of protein

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1

GROMACS version: 2019.4
GROMACS modification: Yes
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I run the script of npt.mdp to simulate the solution process of protein, but the box extend to 40 nm. However, before I run the script of npt, the box was 10 nm when I run the script of nvt.mdp. I wonder whether it is nomal phenomenon the box would be extended larger? The condition of simulating under 298K. The different results of morphology box were upload.

nvt npt

2

Hi JieChen,

This might be related to running the simulation at an NPT ensemble - having a look with gmx energy you migth be able to identify a bit better what is happening.

Changing the pressure coupling protocol might help as well.
Then, just simulation your solvent without protein to check that it has expected properties might be another next step to take.

3

Thanks. I took your advice having a look with gmx energy. I found the charge in box was not neutralized. Then, I tried to extend the box volume to 20 nm and neutralized the charge. The result obviously better than before.