<div dir="ltr">Dear Devels,<div><br></div><div>We've been running some of our usual absolute binding free energy calculations using distance, dihedral, and angle restraints, this time on a larger system than normal (100k+ atoms).</div>
<div><br>What we've found in this situation is that we get crashes reliably due to the dihedral restraints when running with domain decomposition. The errors are typically not helpful (LINCS warnings preceding a crash, sporadic domain decomposition errors, etc.). However, we've established that these problems apparently go away using particle decomposition.</div>
<div><br></div><div>So, this is to ask: Are there expected issues with dihedral restraints and domain decomposition? (We apply restraints between our ligand and reference atoms in the protein). If what we're doing is not advised, it would be nice to know.</div>
<div><br></div><div>Thanks!<br>David</div><div><br clear="all"><div><br></div>-- <br>David Mobley<br><a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a><br>949-385-2436<br>
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