[gmx-users] Simulated Annealing parameters

[Mark Abraham]

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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