[gmx-users] Avoiding calculation on some degrees of freedom

[Anton Feenstra]

David van der Spoel wrote:

> On Tue, 2005-05-17 at 11:56 +0200, gianluca.santarossa wrote:
> 
>>>>For example, if atoms A and B are bonded, and some force
>>>>acts on A, I want to keep the A-B distance constant, 
>>>>moving B
>>>>as much as A, and B not affecting force on A.
>>>
>>>Apart from constraints you mean?
>>
>>Well, AFAIK contraints are not applied on angles or 
>>dihedrals.
> 
> You can constrain angles using a MDP option.

In addition, you can define your own explicit constraints in the 
topology file. In addition, you can define atoms as 'dummies', which do 
not have any degree of freedom of their own, but their position is 
constructed from a set of real atoms, and forces on the dummies are 
redistributed on these real atoms. In effect, what remains of the atom 
when you make it a dummy, are the non-bonded interactions (charge & 
VdW). For hydrogens in biomolecules, this can be done automatically by 
pdb2gmx.

More complicated constructions can be made, for e.g. something like a 
benzyl group you can keep three of the carbons as real atoms, increasing 
their mass to include the mass of the other 'dummified' atoms, define 
constraints between these three to keep them fixed and then define the 
other three carbons and all hydrogens as dummy atoms (which have no 
degrees of freedom and thus are by definition massless!).

There are sections in the manual on this, one in the Topology chapter, 
and one in the Forcefields chapter. Also, you can have a look at:

K. Anton Feenstra, Berk Hess and Herman J. C. Berendsen. "Improving 
Efficiency of Large Time-scale Molecular Dynamics Simulations of 
Hydrogen-rich Systems." (1999) J. Comput. Chem. 20 (8), 786-798
www.few.vu.nl/~feenstra/articles/jcc-20-8-789-798-(1999).pdf


-- 
Groetjes,

Anton

* NOTE: New Phone & Fax numbers (below) *

  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|