[gmx-users] fixed dihedrals

[Anton Feenstra]

From: Bert de Groot <bgroot at gwdg.de>
> 
> Christoph Freudenberger wrote:
> 
>>No idea how easy/difficult that might be and which consequences
>>might arise from that kind of construstions.
>>
>>BTW... how is this implemented in other MD-Packages?
>>I frequently read in the comp. sections of MD-papers that
>>the molecules have been kept rigid using shake (or whatever) with no
>>further details given. Is this always a distance based approach
>>like in gromacs, or are there dihedral/planar constraints already
>>implemented?

Without any further explanation, one must assume that they do exactly
what we also do: keep bond distances fixed. But, I've also heard of
constructions where an out-of-plane mass is added, with constraints
to all the in-plane atoms. Problem there is, of course, as with the
'masses + dummies' constructions, the change in rotational behaviour.

> I don't know about other MD packages, but the algorithm for planar groups
> in the latest Concoord version does just that: project atoms back onto a 
> pre-defined plane. If the plane itself is free to move (but the atoms should
[...]
> I guess it might be a bit of a pain to implement it in gmx, though. Not
> so much for the actual corrections, but more for defining the geometry, 
> because it would require a whole new kind of definition of the planar 
> groups in the topology, that would need to be read/parsed etc.

Well, the actual corrections also will be a pain, since in MD we have
to worry about energy conservation, and having the proper constraint
forces. (I assume you don't need to take that into consideration for
concoord.) Also, the combination with 'normal' constraints and also with
dummy atom constructions should be thought through. These things tend
to be unexpectedly non-trivial, take for example the effects that may
occur for an atom 'in the plane' that is bonded (and hence constraint)
to an atom outside the plane; the plane definition, the atom projection
and the constraint are all inter-dependent.

The actual topology file syntax and parsing could be similar to that
of exclusions: simply a list of all atoms that should be in the plane.
The code to do that is already there; we simply add a new function.
Unless you want to have different sets of atoms to define the plane
and to be projected into it, but that doesn't make sense to me.

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|