[gmx-users] fixed dihedrals

[Anton Feenstra]

Christoph Freudenberger wrote:
> 
[...]
> What do you accually mean with "tight improper"...? It cannot be one
> with a large force constant from your last mail.

But, that actually is what I meant. When shake fails, your only
other choice simply is an improper. If you need the constraint
to be tight, i.e. with only small deviation allowed, you will
need a high forceconstant, and possibly a (very) small timestep.

> Yes, linearity can quite easily be accieved by a construction
> similar to the one i proposed for acetonitrile. Planarity still
> remains a real challenge, mainly because it is quite difficult to
> redeistribute the masses in a way that doesn't disturb the
> tensor of inertia too much. Ok, as an residue within a protein
> this is sure not such a big problem, but for planar slovents
> it is definitly important. Forunatly DMSO isn't planar ;-)

Yes - I made a planar mass+dummy construction for tryptophane.
Wouldn't trust it as a solvent but runs fine as a residue ;-)

But, what I actually meant is a *new* type of constraint that projects
atoms back onto a pre-defined plane, like shake/lincs project atoms
back onto the bond at the right distance.


-- 
Groetjes,

Anton
 _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | (Arrested Development)                                |
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