[gmx-users] atoms

[Anton Feenstra]

Dinesh Pinisetty wrote:
>   Please tell me what they stand for and why there is a difference in the
> atom types between the structure and in the file.
> I hope you got what I mean.Thanks a lot in advance..........

If it is about lipids.itp, ask Peter Tieleman, or look up his papers.
If it is about the Gromos forcefield (or any of the others), try the
Gromos manual that describes the forcefield in high detail, and/or
look up the Van Gunsteren group's papers.

The general gist is that atom types represent atoms with different
behaviour. In principle one would only want one type for carbon, one
for nitrogen and so on, but in practice for, e.g. aromatic carbons,
aliphatic carbons and carbons in lipid tails, three different sets
of parameters are needed. Bond, angle & dihedral parameters are even
more context dependent.

So, atom types don't 'stand for' anything. They are simply a necessity
to getting a forcefield that describes the system well enough. There is
nothing more to it that the different sets of parameters that are
associated with the atom types.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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