[gmx-developers] ridged aromatics

[Anton Feenstra]

Erik Lindahl wrote:

> Hi,
> 
> The forcefield dependencies were solved quite a while ago by  
> introduction of a dummy database file (.ddb) for each FF. If there  are 
> any other issues it is time to open a bugzilla entry so we have  the 
> problem documented.
> 
> However, I would personally recommend against using dummy aromatics.  
> IIRC, the energy conservation checks were mainly compared to normal  
> cutoff simulations where you have huge losses anyway. The proper way  to 
> test it (which is possible now, since we allow rlist>rcoulomb, or  using 
> PME) is to check for energy conservation in the integration.

My initial checks were with isolated residues in vacuum, either without 
cutoff at all, or with a cutoff larger than the size of the residue 
(which amounts to exactly the same: all interactions are always 
calculated). With such a small system and no T/P coupling, any 
conservation error shows up quickly.

Nevertheless, I agree with you: 'dummy aromatics' may be a good idea, 
but they have not been tested thoroughly enough (yet?).


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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