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

Erik Lindahl erik.lindahl at gmail.com
Fri Apr 8 06:56:53 CEST 2022

Hi Kaifang,

Developers tend to get a bit touchy when people use this list (intended for
development & code issues) to get support when they didn't get feedback on
the forums, so please ping and/or provide a more detailed update there



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
> <https://gromacs.bioexcel.eu/t/how-to-avoid-the-molecules-being-too-close-together-in-multiple-molecules-md-simulation/3765>,
> 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.
> --
> Best,
> 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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