[gmx-users] Water residence time

[Anton Feenstra]

David wrote:
> On Tue, 2003-05-06 at 19:10, Andrea Bernini wrote:
> 
>>Dear gmx users,
>>	I would like to compute residence time of water molecules on a protein 
>>surface using a md trajectory of a solvated system. Is it possible to 
>>carry out such calculation using Gromacs tools?
> 
> Yes, check out g_hbond. You'll have to do it in two steps.

It will only look at hydrogen bonded waters.

>>If not, is it possible to obtain a list of water molecules that are 
>>closer than a given distance to the protein for each frame?
> 
> Yes, using trjorder

or g_mindist, using a cut-off distance it will give you the number of
residues (in this case, water molecules), within that distance to a
reference group (which would be your protein).


-- 
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)                               |
|_____________|_______________________________________________________|