On 17/12/2010 3:38 AM, Ehud Schreiber wrote:
Dear fellow GROMACS users,
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).
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.
Mark
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