<div dir="ltr">Dear Developers, <br clear="all">    I want to perform a  protein-ligands system MD simulation. Unlike 
conventional MD simulations, the <span class="gmail-Lm gmail-ng">ligand</span> 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. <br><div>    I tried to use <strong>[distance restraints]</strong> to control the spacing between small molecules,which seems to be achieved by forming a bond between a pair of atoms. However,  <span class="gmail-VIiyi" lang="en"><span class="gmail-JLqJ4b gmail-ChMk0b"><span class="gmail-Q4iAWc">this would lead to a paradox that  bond <span class="gmail-VIiyi" lang="en"><span class="gmail-JLqJ4b gmail-ChMk0b"><span class="gmail-Q4iAWc">often exceeds half of the box during the simulation,  <span class="gmail-high-light-bg">then GMX would exit. such as &quot;The longest distance involved in such interactions is 4.376 nm which is above half the box length &quot;.</span></span></span></span></span></span></span></div><div><span class="gmail-VIiyi" lang="en"><span class="gmail-JLqJ4b gmail-ChMk0b"><span class="gmail-Q4iAWc"><span class="gmail-VIiyi" lang="en"><span class="gmail-JLqJ4b gmail-ChMk0b"><span class="gmail-Q4iAWc"><span class="gmail-high-light-bg">    <span class="gmail-VIiyi" lang="en"><span class="gmail-JLqJ4b gmail-ChMk0b"><span class="gmail-Q4iAWc">I&#39;ve turned to the <a title="http://gromacs.bioexcel.eu/" class="external" rel="external nofollow" href="https://gromacs.bioexcel.eu/t/how-to-avoid-the-molecules-being-too-close-together-in-multiple-molecules-md-simulation/3765" target="_blank">GROMACS user forum</a>, but no one seems to have a good idea.  I</span></span></span></span></span></span></span> sincerely hope that you can give some advice and always look forward to your reply.<br></span></span></span></div><br><div dir="ltr"><div><br></div></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div>Best,</div><div><br></div><div>Kaifang Huang</div><div>New York University</div><div><br></div></div></div></div>