[gmx-users] g_select vs trjorder

[Justin A. Lemkul]

leila karami wrote:
> Dear Justin
> 
> Thanks for your reply.
> 
> 
> I know, with g_select, I obtain index groups that tell me which atoms 
> satisfy the given criteria and with trjorder, the coordinates of those 
> atoms are reordered such that they are listed in sequence in the new 
> trajectory. But g_select gives an output file (size.xvg) and trjorder 
> gives an output file (nshell.xvg). Both of these output files contain 
> number of atoms satisfy the given criteria. In my case these number are 
> not the same at the special frame. Why?
> 

 From g_select -h:

"With -os, calculates the number of positions in each selection for each
frame."

 From trjorder -h:

"With option -nshell the number of molecules within a shell of radius -r
around the reference group are printed."

Thus the two output files should not be equivalent.

-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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