<div dir="ltr">Hi Kaifang,<br><div><br></div><div>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 instead.</div><div><br></div><div>Cheers,</div><div><br></div><div>Erik</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Apr 8, 2022 at 3:59 AM Kaifang Huang <<a href="mailto:kh3687@nyu.edu">kh3687@nyu.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">Dear Developers, <br clear="all"> I want to perform a protein-ligands system MD simulation. Unlike
conventional MD simulations, the <span>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 lang="en"><span><span>this would lead to a paradox that bond <span lang="en"><span><span>often exceeds half of the box during the simulation, <span>then GMX would exit. such as "The longest distance involved in such interactions is 4.376 nm which is above half the box length ".</span></span></span></span></span></span></span></div><div><span lang="en"><span><span><span lang="en"><span><span><span> <span lang="en"><span><span>I've turned to the <a title="http://gromacs.bioexcel.eu/" 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"><div dir="ltr"><div>Best,</div><div><br></div><div>Kaifang Huang</div><div>New York University</div><div><br></div></div></div></div>
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