<div dir="ltr"><div><div><div>Hi, Berk, Eric,<br><br></div>By "special" bonds, angles, and dihedrals, I just mean simple harmonic bonds, angles, and dihedrals, as already implemented in GROMACS.<br><br></div>Yes, by "stability problems" I mean "unstable". <br>
<br></div>We are not running with velocity verlet here. We also do not have inter charge-group constraints, if I remember correctly.<br><div><br>We have successfully verified in this system that simulations run stably to completion when we run in serial, but we reliably get crashes in parallel.<br>
<br>I will submit a Redmine. I'm getting input files from my student so it may take a little bit. Please note that you will likely have to run a while to get the crashes -- these are not immediate; we're always able to minimize successfully and get some distance into actual dynamics. As I mentioned it's a stability problem.<br>
<br>David<br><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Mar 18, 2014 at 12:58 AM, Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi,<br>
<br>
What do you mean with "special" bonds, angles and dihedrals? Are
these potentials you coded yourself?<br>
I assume that with "stability problems" you mean that things are
unstable, not that the simulation stops with a fatal error because
it can't find atoms in interactions.<br>
<br>
If you are using the velocity verlet integrator with inter
charge-group constraints, that can give issues in parallel. I just
uploaded a fix to gerrit for release-4-6.<br>
<br>
Cheers,<br>
<br>
Berk<div><div class="h5"><br>
<br>
On 03/18/2014 07:04 AM, Erik Lindahl wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<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" target="_blank">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): <a href="tel:%2B46%208%20524%2081567" value="+46852481567" target="_blank">+46 8 524 81567</a></div>
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</div>
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<div><br>
On Mar 17, 2014, at 6:51 PM, David Mobley <<a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<div dir="ltr">
<div>
<div>
<div>
<div>Dear Devs,<br>
<br>
</div>
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>
<br>
</div>
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>
<br>
</div>
<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>
<br>
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.
<br>
</div>
<div><br>
</div>
<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>
<br>
Thanks!<br>
</div>
<div><br>
</div>
Reference:<br>
<a href="http://dx.doi.org/10.1021/jp0217839" target="_blank">http://dx.doi.org/10.1021/jp0217839</a><br>
<br>
</div>
<div>
<div>
<div>
<div>
<div><br>
-- <br>
David Mobley<br>
<a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a><br>
<a href="tel:949-385-2436" value="+19493852436" target="_blank">949-385-2436</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
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