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Dear developers,<br>
<br>
within my simulations, I encounter the problem, that I have to save
the forces and velocities of the whole system, even though I need
only those for very few atoms (in my case: a small particle e.g. a
fullerene, further details: see below). This generates a lot of
unnecessary data and also slows down the simulation a lot, as I have
to write out the trajectory every step (2 fs).
<br>
A possible solution would be to write forces and velocities only for
a group of atoms, as is possible for the compressed trajectory for
positions (.xtc). So far, I did not find any possibility doing that
and also no upcoming features.
<br>
<br>
Did I miss anything? If no, is this, or a similar functionality
planned for a future release?
<br>
If neither of this, is there a chance to do it myself, ether only
for my personnel use or as an official contribution?
<br>
<br>
Kind regards,
<br>
Andreas Baer
<br>
<br>
<br>
Some further details to my simulation:
<br>
A nanosized particle (artificial or fullerene) is dissolved in a box
of solvent (10<sup class="moz-txt-sup"><span
style="display:inline-block;width:0;height:0;overflow:hidden">^</span>5</sup>
to 10<sup class="moz-txt-sup"><span
style="display:inline-block;width:0;height:0;overflow:hidden">^</span>6</sup>
molecules). Transport coefficients should be calculated using the
Green-Kubo formalism. Thus, velocities and forces are required at a
very high frequency, so that I write out every step. As I only need
the information for the particle, I get a huge amount of unused
data, that I have to postprocess, to retrieve the desired
information. The biggest problem is, that this slows down my
simulation by a factor of roughly 20, depending on the hardware
used.
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