[gmx-users] Simulated Annealing

[Anton Feenstra]

Periole Xavier wrote:
> 
> 
> 
> Hi,
> 
> the temperature is expressed in K ... - 1000 theorically doesn't
> exist.
> I wouldnt be suprised that the problem comes from the negative
> cinetic energy your generate a t=0.
> 
> Try zero_temp_time = 0
> 
> By the way you have to make another minimization before the
> simulated annealing to get the (approximated) 0 K temperature.

No, you have things mixed up. zero_temp_time sets the *time* at which
the temperature would be zero. z_t_t=-1000 would have your simulation
be 0K at t=-1000ps, and ref_t K at t=t_init ps. The actual reference
temperature for the simulation goes along the straight line through
these points. This is conceptually a bit involved, but IMHO it is
clearer than providing a heating or cooling rate in K/ps.

See also the FAQ (it has two example temperature 'graphs')
"Why do I get very strange temperatures in simulated annealing?":
http://www.gromacs.org/faq/index.php#temp

By the way, there is no intrinsic problem in generating a -1000K
velocity distribution: all velocities will simply be negative, i.e.
pointing the 'other' way which doesn't matter since they're random
anyway... ;-) Physically, ofcourse, that doesn't correspond to a
-1000K ensemble of atoms... :-O

-- 
Groetjes,

Anton
 ________ __________________________________________________________
|        | Anton Feenstra                                           |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam   |
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