[gmx-developers] How to avoid the molecules being too close together in multiple molecules MD simulation?
erik.lindahl at gmail.com
Fri Apr 8 06:56:53 CEST 2022
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On Fri, Apr 8, 2022 at 3:59 AM Kaifang Huang <kh3687 at nyu.edu> wrote:
> 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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Erik Lindahl <erik.lindahl at dbb.su.se>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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