[gmx-developers] How to avoid the molecules being too close together in multiple molecules MD simulation?

Kaifang Huang kh3687 at nyu.edu
Fri Apr 8 03:59:11 CEST 2022

Dear Developers,
    I want to perform a protein-ligands system MD simulation. Unlike
conventional MD simulations, the ligand were not put into the binding
pocket, but I copied many ligands and put them around the protein to run
MD. But, during MD, I found a fatal problem, that is, many ligand Molecules
tend to clump together.
    I tried to use *[distance restraints]* to control the spacing between
small molecules,which seems to be achieved by forming a bond between a pair
of atoms. However,  this would lead to a paradox that  bond often exceeds
half of the box during the simulation,  then GMX would exit. such as "The
longest distance involved in such interactions is 4.376 nm which is above
half the box length ".
    I've turned to the GROMACS user forum
but no one seems to have a good idea.  I sincerely hope that you can give
some advice and always look forward to your reply.


Kaifang Huang
New York University
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