GROMACS version: 2019.6
GROMACS modification: No
I am doing simulation of 2 proteins, one is a protein fibril having 5 chains and another is the unfolded monomer, there are total 740 residues. After nvt equillibration the protein is going out of the water box. I have taken a truclinic box, having 3.3 lakh atoms. How to solve the issue? I am attaching the image of the .gro file got from nvt.
Either increase the size of the box or try doing -pbc mol.
Your box is too small and it’s shape is too reflective of the initial geometry and not it’s rotational symmetry. If your protein rotates over time, it will violate the minimmm image convention and interact with itself. You need a box that is at least large enough in all spatial dimensions to accommodate the longest dimension of the protein. You can use a rhombic dodecahedral box to save on the number of waters relative to a cubic box.
Note that there is no “outside” if a periodic system so if the solute cannot be consistently rewrapped into the central image, it usually means the box is inappropriate for the system being studied.
I tried with dodecahedron box, that contains 9 lakh atoms and it will increase computational cost. The performance was like 3ns/day, is there any other way to do this…
MD simulations are computationally expensive. If you want to simulate a large, elongated solute molecule, you have to accept that you need to accommodate it in a large box with lots of water.
Okay sir, i got it, thank you so much.