[gmx-users] Rigid body optimization

[Anton Feenstra]

Mengjuei Hsieh wrote:
> Hi,
> 
> I want to confirm that the all-angles constraints in gromacs is almost not
> usable. I tried lots of times trying to figure out. The problem might be
> related to whether or not the starting structure is built with ideal
> geometries. This might not be a bug, but a feature instead. Angle
> constraints are very complicated and very hard to iterate to reach under the
> tolerance if we use SHAKE/LINCS algorithm.
> 
> Perhaps we need constraints according to the starting structure, not ideal
> angles/lengths like what CHARMM does.
> 
> Any idea?

First off, all-angle constraints will fail with LINCS, LINCS cannot handle
that type of contraints at all.

Second, it wouldn't be too hard to write a script that parses out all
relevant constraint pairs (i.e. for bond and angle restraints), gets
the appropriate actual distances from your starting conformation, and
writes that back into your topology as the constraint distance.

Come to think of it, since the goal of the exercise was to simulate
proteins (or parts) as rigid bodies, it may be better to define
constraints in order to get make the protein rigid, meaning probably
that you would want an additional number of constraints next to the
bond and angle contraints themselves, e.g. between i-i+4 partners
in a helix, and other close contacts that define the 3d structure.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Room P275  Tel: +31 20 44 47608  Fax: +31 20 44 47610 |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "Everybody is Smashing Things Down" (Offspring)       |
|_____________|_______________________________________________________|