[gmx-users] g_select vs trjorder

[Justin A. Lemkul]

leila karami wrote:
> Dear all
> 
> Which one of g_select and trjorder is the best for obtaining those water 
> molecules being within x nm of protein?
> 

You will have to define what "obtaining" means.  The tools you've mentioned do 
different things.  With g_select, you obtain index groups that tell you which 
atoms satisfy the given criteria.  With trjorder, the coordinates of those atoms 
are reordered such that they are listed in sequence in the new trajectory.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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