[gmx-developers] ridged aromatics
feenstra at few.vu.nl
Mon Aug 8 09:27:01 CEST 2005
David van der Spoel wrote:
> On Fri, 2005-08-05 at 09:55 -0400, Ken Rotondi wrote:
>>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 ).
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