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On 17/12/2010 3:38 AM, Ehud Schreiber wrote:
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<p class="MsoNormal">Dear fellow GROMACS users,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am using the simulated annealing option
in gromacs 4.5.2 (in
an implicit solvent all-vs-all setting, by the way), i.e.
using the annealing,
annealing_npoints, annealing_time, annealing_temp parameters
in the mdp file. I
also specify the tcoupl, tc_grps and tau_t parameters for the
temperature
coupling, as well as the gen_vel, gen_temp, gen_seed ones for
initial velocity
generation. The perplexing behavior I’m encountering is that
grompp
requires me to specify also the ref_t parameter although it
would seem to be
overridden by the annealing parameters mentioned above. Am I
doing anything
wrong? If not, the correct behavior would be to warn when this
parameter is
specified rather than to demand it (and then presumably ignore
it).</p>
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<br>
It's easier to write and maintain code that functions the same way
even when something is redundant in a particular case. Making the
.mdp ref_t optional or illegal only when annealing is being used
(when the SA implementation probably copies the SA values to the
memory formerly occupied by the .mdp values) doesn't have enough of
a gain to be worth the cost in coding time and ease of people
understanding the full ramifications of the code. Thanks for the
thought, though.<br>
<br>
Mark<br>
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