[gmx-developers] ridged aromatics

[Ken Rotondi]

Hello all,

I was wondering if the ridged aromatics issues had been addressed in 
the GROMACS 3.3? I realize it's not likely, but you never know...

Thanks as always,

Ken


On Aug 8, 2005, at 3:27 AM, Anton Feenstra wrote:

> David van der Spoel wrote:
>
>> On Fri, 2005-08-05 at 09:55 -0400, Ken Rotondi wrote:
>>> Hi all,
>>>
>>> I was wondering if when GROMACS derives ridged aromatic atoms from 
>>> basis atoms, it includes the derivatives (dE/dxj) (dxj/dij) where j 
>>> is the dependent atom, and if so, where this is stored.
>> check manual on virtual particles.
>>> We may take a shot at debugging this code.
>> to get it in working form again? It is force field dependent as well.
>
> RIght. Unfortunately, some distances were hard-coded (mea culpa), 
> which obviously can create problems with changing forcefields. I'd be 
> happy to provide comments and explanations on the code, if needed.
>
>> Problems could involve the definitions of the dummies and the
>> implementation of the dummy forces.
>
> Possible, but not very likely. Berk Hess derived the formula's, and 
> together we carefully checked all of it. FOr example, isolated 
> aromatic residues in vacuum gave near perfect energy conservation. Any 
> small bug the code would, I think, have shown up pretty fast. Anyway, 
> since strange behaviour of these regid aromatics have been reported, 
> it would be very good indeed if somebody took the time to dive into it 
> again.
>
> Anyway, you may want to start off by checking the actual forumula's, 
> they are in the JCC article ( /J. Comput. Chem./ 1999, *20*, 786-798 ) 
> although the dummyfied aromatics were described only later ( /J. Phys. 
> Chem. B/ 2002, *106*, 8858-8869 ).
>
>
> -- 
> Groetjes,
>
> Anton
>
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> |  _   _  ___,| K. Anton Feenstra                                     |
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