[gmx-users] g_select vs trjorder

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 8 15:42:41 CET 2012

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

 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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