[gmx-users] extract water coordinate from xtc

[Mark Abraham]

SeungPyo Hong wrote:
> Dear gmx-users,
> 
> I want to study the behavior of a certain water molecule near the active 
> site.
> I can convert .xtc file into pdb file, but the file becomes too large 
> when I include all the water molecule in it.
> Maybe I can incooperate only a small portion of water molecule.
> But is there anyother way to extract coordinate from the .xtc file directly?
> 
> This is the procedure what I want to do:
> 1. extract coordinates of a frame.
> 2. analyze it. (Find a water molecule of interest and ...)
> 3. extract coordinates of the next step.
> 4. goto 2. until finish

Read section 7.4 of the manual, please. There's a utility that does 
this, and the list of utilities there will suggest to you where to look 
further to solve your own problem.

Mark