[gmx-developers] dynamic topology
feenstra at chem.vu.nl
Tue Oct 28 09:50:12 CET 2003
Jason DeJoannis wrote:
> 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 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.
| | |
| _ _ ___,| 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/ |
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