[gmx-users] the neighbour getting

[K.A. Feenstra]

Erik Lindahl wrote:
> 
> alexander yakovenko wrote:
> > Hi All,
> >
> > Does you know how to get the neighbour molecules from the trajectory file?
> > I need to make the .ndx file with the group of water molecules, which located
> > no more than 5A from residue 1 of my protein.
> 
> Just write a small analysis program that calculates it directly from the
> coordinates. In theory you could of course dump the neighborlist from
> Gromacs, but since that extends to 10A it will be much longer (and
> written every 10 steps).

Better stil: there is the program trjorder, which can sort your water 
molecules in order of distance from the protein. Then, you can select 
the first so many water molecules that will make up your 0.5nm layer of 
water. See trjorder manpage for more info:
http://www.gromacs.org/documentation/reference_3.0/online/trjorder.html

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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