[gmx-developers] dynamic topology

[Anton Feenstra]

Jason DeJoannis wrote:

> Hi,
> 
>   Good, that worked. In fact I took advantage of 
> the *mdatoms=atoms2md() to copy top->atoms to mdatoms. 
> It would be more efficient to copy only the atoms that 
> change but I am not worried about that right now.
> 
>   Do you have any remarks about a more complex topology
> change? For example, what if I wanted to simulate mutation 
> in an O2/Argon mixture (I'll stay away from charged groups 
> for now). I am not sure how to proceed with polyatomic
> molecules in other words. I am thinking that maybe I
> have to delve into top->blocks[1] somehow.
> 
>   Another thing. How can I access basic properties for a
> specific atom-type? I have looked and looked for a structure
> that does this. Perhaps I should make my own. top->symtab is 
> not easy to understand. For example, lets say I wish to know 
> the standard mass and atomname for atom-type 'i'. For the 
> atomname I would need a formula which converts i into an 
> address for the corresponding string inside top->symtab.

These things are in top->atoms, but IIRC not in mdatoms (for
performance reasons). Mass is in mdatoms, though.

symtab is a construction mainly to preserve memory, so that
each atom- or residuename is stored only once. So, all entries
in top->atomname (check exact structure syntax) and top->resname
refer to symtab instead of having each a separately allocated
area of memory for the name info.


-- 
Groetjes,

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