<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Hi David,</div><div><br></div><div>It's virtually impossible to say without a specific example, but of course things should work fine in parallel too.</div><div><br></div><div>Create a redline and upload a specific example where you get different results or a stability issue and describe the _exact_ conditions so it can be reproduced.</div><div><br></div><div>Cheers,</div><div><br></div><div>Erik<br><br>--<div>Erik Lindahl <<a href="mailto:erik.lindahl@scilifelab.se">erik.lindahl@scilifelab.se</a>></div><div>Professor of Biophysics</div><div>Science for Life Laboratory</div><div>Stockholm University & KTH</div><div>Office (SciLifeLab): +46 8 524 81567</div><div>Cell (Sweden): +46 73 4618050 </div><div>Cell (US): 1 267 307 8746</div><div><br></div></div><div><br>On Mar 17, 2014, at 6:51 PM, David Mobley <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div>
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<div>Dear Devs,<br>
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For many years we have been doing binding free energy calculations with restraints to hold the ligand in the binding site. Lately, however, as we move to bigger systems, we simply can't get these simulations to run stably. Does anyone have experience with using
restraints between relatively distant atoms in parallel simulations? Any encounters with similar problems or suggestions?<br>
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Specifically, we normally use a set of six restraints between the ligand and the protein to restrain the six rigid-body degrees of freedom. These use three reference atoms in the protein and three in the ligand, as described in the reference below. Normally
these atoms are relatively distant from one another, by design.<br>
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<div>We have in the past mostly used distance_restraints, angle_restraints and dihedral_restraints for implementing these. However, these seem to lead to stability problems when we run on a few cores (perhaps 8) as we move to larger systems, and especially
so when using constraints on bonds involving hydrogen. Additionally, since these restraints cannot be applied between 'molecules' in the topology, this means there are technical reasons we prefer another form for the restraints.<br>
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Lately, we have been testing using special bonds, angles, and dihedrals for restraints between these atoms. However, we keep encountering stability problems there as well, at least when running in parallel (we are testing whether running on a single core will
alleviate these). We DO already know that if we take a topology file which will run stably in serial with the old form of restraints, convert the restraints to the new form (bonds, angles, dihedrals) and attempt to run it in parallel we tend to run into problems.
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<div>In any case, does anyone have experience with using restraints between relatively distant atoms, and suggestions on how to get our systems to run stably? For what it's worth, these are systems which run fine in parallel without the restraints, and the
restraints are not unusually strong. (We've run with stronger restraints many times in the past without issues).<br>
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Thanks!<br>
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Reference:<br>
<a href="http://dx.doi.org/10.1021/jp0217839">http://dx.doi.org/10.1021/jp0217839</a><br>
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-- <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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