[gmx-users] water in channel

[Anton Feenstra]

Jocelyne Vreede wrote:

> Dear Itamar and Anton, 
> 
> A while ago I had similar problems with genbox: the program wrongly
> inserted water molecules in a protein. I solved it by clustering water
> molecules on the basis of hydrogen bonds. If a water molecule forms a
> hydrogen bond to a water molecule of the cluster, it is added to the
> cluster, otherwise a new cluster is created. 
> This way, the bulk solvent is represented as one single cluster, whereas
> additional clusters identify water molecules that are isolated i.e.
> inside the protein or lipid bilayer. 
> 
> If you are interested, I can send you the code (in C). 

That sounds wonderfull! I'd very much like to see it, and probably
add it as analysis tool to Gromacs if that's OK with you?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | 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)                               |
|_____________|_______________________________________________________|