[gmx-users] fixed dihedrals

[Anton Feenstra]

Christoph Freudenberger wrote:
[...]
> But is the residual freedom left by the constraints really larger
> than that given by the improper?

That would depend on a lot of details, I'd guess. If Shake convergence
becomes the bottleneck (no experience with that myself, but I know it
*can* sometimes be a problem), you might be better off with a tight
improper and maybe even a shorter timestep. On the other hand, if you
want it constrained (as in 'immobile'), you need a different construction
to completely remove the degree of freedom from your molecule, for
example a construction with three 'masses' and a set of dummy atoms,
as was discussed on the list for some solvent molecule last week.

Otherwise, might we want to implement a planarity constraint?
Is that at all feasible? Or sensible?

[...]
> If you keep angles and or bonds flexible, improper dihedrals
> are the better choice, no doubt about that.

No doubt.


-- 
Groetjes,

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