[gmx-developers] Changed dummy generation in TYR

[Anton Feenstra]

Erik Lindahl wrote:

> Hi,
> 
> When I was playing around with dummy support in OPLS I noticed that the 
> dummy generation in Tyrosine wasn't always stable.
> 
> The problem was that the HH angle was kept constant by introducing a 
> constraint to the CG atom. Since this distance is considerably longer 
> than the constraint OH-HH it caused frequent instabilities unless you

> used lincs_order=8.


Ah, I never considered this... It makes sense, though, that such an
elongated triangle of constraints might not be stable at low lincs
orders. Thanks for checking this!

> I've worked around it by introducing a virtual mass at twice the 
> distance from OH (compared to the OH-HH distance). Half the HH mass
> is put there, and the other half added to the OH atom. The HH bond
> is then recreated as a dummy2 from the OH and virtual mass coordinates.
> 
> This will still increase the HH rotational inertia slightly, but it
> shouldn't be a worse approximation than anything else of the dummy stuff.


Hmm. It already was a pretty dirty construction (or, weird at least),
but this sounds even worse... Though I agree, it probably isn't so bad
an approximation, compared to the rest. The rotational inertia could
be tuned by adjusting the mass distribution over the oxygen and virtual
mass particles (it doesn't need to be half-half).

A nicer solution would be to allow a constraint with a dummy atom, but
I think that would make an additional constraints step necessary. That
is a bit too much for such a small problem...



-- 
Groetjes,

Anton
  ________ ____________________________________________________________
|        | Anton Feenstra                                             |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam     |
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