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<div class="moz-cite-prefix">Hi Christian,<br>
<br>
You may want to have a look at grompy
(<a class="moz-txt-link-freetext" href="https://github.com/GromPy/GromPy">https://github.com/GromPy/GromPy</a>). This is a python wrapper
around the gromacs 4.0.7 library, using direct C-library calls.
One current application is sampling the grand-canonical ensemble
using a hybrid MC scheme.<br>
<br>
The application is published here:<br>
<a class="moz-txt-link-freetext" href="http://onlinelibrary.wiley.com/doi/10.1002/jcc.22947/abstract">http://onlinelibrary.wiley.com/doi/10.1002/jcc.22947/abstract</a><br>
<br>
Best regards,<br>
René<br>
<pre class="moz-signature" cols="72">=====================================================
René Pool
Department of Biological Psychology
Faculty of Psychology and Education
VU University Amsterdam
Van der Boechorststraat 1
1081 BT AMSTERDAM, the Netherlands
Room 2B-05
E: <a class="moz-txt-link-abbreviated" href="mailto:r.pool@vu.nl">r.pool@vu.nl</a>
T: +31 20 598 38 52
=====================================================
</pre>
On 02/13/2013 05:01 PM, Christian H. wrote:<br>
</div>
<blockquote
cite="mid:CAF_d05jKfATx=BKDrQwnfBHdki8zA+pUZ-ieL+9DahbSymHhuQ@mail.gmail.com"
type="cite">
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charset=ISO-8859-1">
Hi,<br>
<br>
I am trying to figure out how one would go about implementing a
simple Hybrid Monte Carlo scheme in GROMACS. For my purposes I am
only interested in the md-vv integrator, using either a NVT or NPT
ensemble. MPI is not a strict necessity, as the system I am going
to look at are probably small.<br>
So far I reversed the order between the energy calculation and the
trajectory output, by keeping a backup of my current configuration
where appropriate. This way I can check whether to accept the
current configuration before anything is written to the trajectory
file.<br>
The point I am struggling with is the overall energy: It seems it
is not sufficient to just deal with enerd->term[F_ETOT] from
md.c. For example if I do an integration step, (thereby changing
the current enerd->term[F_ETOT]) and then decide to reject it
(setting enerd->[F_ETOT] = previousEnergy and copying back the
previous state->x), a different value than previousEnergy is
written to the .edr file.<br>
<br>
I guess the actual energy output takes place in print_ebin of
mdlib/mdebin.c, or more precisely do_enx of gmxlib/enxio.c. I
can't really make out of this works though. Is there any detailed
information about the file format available somewhere? It seems
like either enerd->term[F_ETOT] from md.c is not directly used
and/or the total energy is recalculated somewhere along the way.<br>
If anybody sees a glaring error in my approach in general, please
point it out as well - I am really new to the GROMACS source and
have only a rough understanding of how it works overall. <br>
<br>
Thanks,<br>
Christian<br>
</blockquote>
<br>
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