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Please excuse me - for some reason the axis labels in the
buffer-size vs- energy-drift plot got lost.<br>
Here is the complete plot:<br>
<a class="moz-txt-link-freetext" href="https://www.dropbox.com/s/otuijs1py55zmzh/buffersize-vs-total-energy-drift-1.png?dl=0">https://www.dropbox.com/s/otuijs1py55zmzh/buffersize-vs-total-energy-drift-1.png?dl=0</a><br>
<br>
<div class="moz-cite-prefix">Am 21/07/15 um 14:40 schrieb Bernhard:<br>
</div>
<blockquote cite="mid:55AE3DCE.4010205@uni-kassel.de" type="cite">
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Dear Michael,<br>
<br>
thank you very much for your very helpfull answer.<br>
Obviously we agree on the dubious nature of the linear drift and
that its origin from reduced precision round-off errors is
doubtful.<br>
In my opinion the occurence of a linear energy drift of this size
could indicate a bug in the program.<br>
So I startet a more rigorous investigation and would like to share
some preliminary results:<br>
<br>
Graph of Verlet buffer-size vs. energy-drift size for single and
double precision:<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://www.dropbox.com/s/e56916inlm0ym48/buffersize-vs-total-energy-drift.png?dl=0">https://www.dropbox.com/s/e56916inlm0ym48/buffersize-vs-total-energy-drift.png?dl=0</a><br>
<br>
Graph of the linear total energy drift for a buffer-size of
0.02nm:<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://www.dropbox.com/s/ifq3v3jwfzn4goh/4_nve_100ps_rlist-1.02_Total-Energy.png?dl=0">https://www.dropbox.com/s/ifq3v3jwfzn4goh/4_nve_100ps_rlist-1.02_Total-Energy.png?dl=0</a><br>
<br>
Exemplary mdp and log files for a buffer-size of 0.02nm:<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://www.dropbox.com/s/peamt27d2exhclc/4_nve_100ps_rlist-1.02.mdp?dl=0">https://www.dropbox.com/s/peamt27d2exhclc/4_nve_100ps_rlist-1.02.mdp?dl=0</a><br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://www.dropbox.com/s/70ictqb6nbs94wk/4_nve_100ps_rlist-1.02.log?dl=0">https://www.dropbox.com/s/70ictqb6nbs94wk/4_nve_100ps_rlist-1.02.log?dl=0</a><br>
<br>
The investigated protein-water system consists of 22765 atoms, the
AMBER99SB-ILDN force field with TIP3P water was used, all
simulations were in the NVE-ensemble, GROMACS 4.6.7 was used.<br>
<br>
I will repeat the tests with GROMACS 5.0 and for different test
systems (i.e. the lysozyme system from the popular lysozyme
tutorial of Justin Lemkul).<br>
<br>
Best,<br>
Bernhard<br>
<br>
<div class="moz-cite-prefix">Am 20/07/15 um 00:50 schrieb Shirts,
Michael R. (mrs5pt):<br>
</div>
<blockquote
cite="mid:D1D19173.6F07F%25mrs5pt@eservices.virginia.edu"
type="cite">
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<div>> Do I have to switch to double precision if I care
about energy conservation, integrator symplecticity, phase
space volume conservation and ergodicity?</div>
</div>
<div><br>
</div>
<div>This sounds a like a good idea. If you are doing tests
where this matters, use double precision. Sounds like the
safest. </div>
<div><br>
</div>
<div>> Since bigger round-off errors by reduced precision
shouldn't accumulate linearly but at worst with Sqrt(N):
Shouldn't one be worried about the occurence of a linear
systematic error by only changing the precision from double
to single in a calculation?</div>
<div><br>
</div>
<div>Reduced precision errors only would be linear if the
errors are uncorrelated, but it's not clear to me why
roundoff errors would be uncorrelated.</div>
<div><br>
</div>
<div>> But if you have a constant downward drift of energy
you must consider that there is less phase space volume at
lower energies - so there is no volume conservation in phase
space.</div>
<div><br>
</div>
<div>Correct, for NVE. For NVT, the conserved energy is a
bookkeeping number, it has nothing to do with the current
phase space of the system. The thermostat is pumping in more
energy so that the kinetic energy remains consistent with
the desired temperature. We then actually have a steady
state system, rather than an equilibrium system. The
question is, how different is this distribution from the
true equilibrium distribution? </div>
<div><br>
</div>
<div>This is generally testable. For
thermodynamic calculations (which is what one presumably is
intrested in with a thermostat, rather than the dynamics ),
what really matters is 1) whether the correct distribution
is obtained within noise and 2) whether the sampling is
ergodic. 2) is very hard to answer, but 1) can be checked
by </div>
</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="https://github.com/shirtsgroup/checkensemble">https://github.com/shirtsgroup/checkensemble</a></div>
<div><br>
</div>
<div>With the theory described here:</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://dx.doi.org/10.1021/ct300688p">http://dx.doi.org/10.1021/ct300688p</a></div>
<div><br>
</div>
<div>Gromacs in single precisions seems to behave fine
statistically for systems of a few hundred atoms.</div>
<div><br>
</div>
<div>I suspect that there are subtle phenomena where the lack of
exact symplecticness matters. I also believe from my testing
(no full paper on this) that there aren't very many that occur
in highly chaotic systems with hundreds of particles at NIT. </div>
<div><br>
</div>
<div>I bet there are cases with just a few particles where the
problems could become very obvious, however.</div>
<div><br>
</div>
<div>Best,</div>
<div>~~~~~~~~~~~~</div>
<div>Michael Shirts</div>
<div>Associate Professor</div>
<div>Department of Chemical Engineering</div>
<div>University of Virginia</div>
<div><a moz-do-not-send="true"
href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a></div>
<div>(434) 243-1821</div>
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