[gmx-users] fixed dihedrals

[Bert de Groot]

Christoph Freudenberger wrote:
> 
> Anton Feenstra wrote:
> > 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.
> 
> 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?
> 


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
not move with respect to the plane), this means that the definition of the
plane must be updated every step (in Concoord this is done by taking the 
best-fitting plane through the uncorrected positions, to guarantee a 
minimal correction). I don't know how useful it would be in  MD, but in 
Concoord this algorithm results in faster convergence and improved 
planarity as compared to the more usual approach using impropers.

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.

--

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________