GROMACS version: 2018, 2020
GROMACS modification: No
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Dear colleagues,
I am simulating four proteins (in mixture with water and drug molecules) undergoing thermal annealing to accelerate “mixing” of the box. However, some distance restraints would be necessary to prevent protein unfolding, while letting each of them move as a whole molecule. If I use “gmx genrestr -disre” for 1 protein it works perfectly: Rg remains the same throughout the annealing stage. I can also apply it to 1 protein and 1-2 small molecules (haven’t tried more), seems to work equally fine. However, when more than 1 protein is restrained exactly the same way, gmx mdrun comes with an error:
Assertion failed:
Condition: type_max - type_min + 1 == dd->nres
All distance restraint parameter entries in the topology should be consecutive
I am wondering what can cause such problem. As far as I understand, the difference between running few small restrained molecules and few restrained proteins is that the later ones consist of multiple residues each (or just generally bigger, but that should not be the case, as I only restrain proteins’ C-Alpha, which is close to the number of atoms in the small molecule). Would some renaming-relabelling help, or that should not be the cause of the issue?
I tried both “Protein 4” and “Protein1 1, Protein2 1; Protein3 1; Protein4 1” in the topology, where each of the four would refer to the identical .itp files (except the [moleculetype]) and restraint files with the numbers of the atoms in a single molecule.
Also, as an alternative, - would it be reasonable to couple proteins to another thermal bath (with room temperature) while the small molecules are being heating and cooled again?
If anyone can comment any of the/both questions, it would be highly appreciated!
Thanks,
Aleksei