How to deal with high concentrations of ligands in gromacs

User discussions
1

GROMACS version: 2021.2
GROMACS modification: No

Hello,
I am trying to do modeling of a protein with high concentrations of free ligands (more than 100 molecules), is there any way to confer a repulsive potential to prevent aggregation of each of these ligands?

Please help me for solving this problem.
Thanks for your kind advice.
Kind regards,

2

Depending on the nature of the co-solutes, how well they are parametrized, and the effective concentration, you may be observing real behavior. That should be the first question - is it necessary to apply such a potential?

3

I fully understand what you’re talking about.
But, I just want to know if there are any technical options to give repulsive force in this situation.
for example, I tried to use distance restraints but it looks inefficient to apply to every combinations of hundreds of ligands.

Thank you,

4

Construct a virtual site at the center-of-mass of each molecule and use [nonbond_params] to apply a repulsive LJ potential between just those virtual site particle types.

5

Thank you so much for your kind advice. I will try as you guided.