[gmx-developers] ridged aromatics

[Erik Lindahl]

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.

Energy conservation is an absolute measure - if it isn't perfectly  
conserved when you use a conservative (in the mathematical/physics  
meaning) potential you're using too long timesteps.

Now, on balance, I'm not saying dummy aromatics are bad either - just  
that they haven't been tested enough :-)

Cheers,

Erik


On Sep 21, 2005, at 11:15 PM, Ken Rotondi wrote:

> 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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