[gmx-developers] Re: Adding an artificial energy term for structure refinement

[Anton Feenstra]

On 16/08/12 10:22, alex.bjorling wrote:
> Forgot to mention that the artificial energy term would of course be based on
> some running average of predicted scattering, not the predicted scattering
> of individual frames. My question remains, though, of whether GROMACS needs
> explicit forces.

The short answer is: yes.

But you are not clear on what you want to achieve.

Do you want to generate an ensemble of conformations that are compatible 
with your experimental data?

Or do you want to simulate your physical system and evaluate the match 
with your experimental data?

In the first case, perhaps a Monte-Carlo approach is more suitable.

In the second case, you don't need those artificial forces. Just run 
your simulation and trust that Newtonian mechanics gets 'the 
time-averaging right' as well as 'the fitted structures make some 
mechanical sense'. ;-)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Free University  Amsterdam     |
|(   |   )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands  |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "Every Sperm is Sacred" (Monty Python)                |
|_____________|_______________________________________________________|