[gmx-users] fixed dihedrals

[Anton Feenstra]

Christoph Freudenberger wrote:
> Gerrit Groenhof wrote:
> 
>>>
>>> Dear all,
>>>
>>> is it possible to fix single dihedral angles
>>> during a MD run. If yes, what's the easiest
>>> way of implementation?
>>
>> You can use an improper dihedral. Using a proper dihedral with a too
>> strong potential might result in integration errors I think.
> 
> If the rest of the molecule is already constrained (all-angles) you might
> be able to use to more constraints. for a molecule like
> 
>     -1       4-
>       \     /
>        2---3
>       /
>     -5
> 
> you can add constraints for 1-4 and 5-4 to fix the diehd.

That will *not* keep your dihedral fixed! Within the limits
of a constraint, there is still considerable freedom for the
dihedral angle to fluctuate (it's easy to calculate if you
remember your goneometry lessons). For the Shake constraints
algorithm, this construction will be hard to converge, and
for Lincs it will probably not even be possible to use it
(too many connected constraints).

So - the only way to do it *is* adding an improper, and *yes*,
setting the force constant high will give high frequencies in
the motion in this angle, and can result in integration errors
and ultimately a simulation crash.


-- 
Groetjes,

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