[gmx-users] g_order in GROMACS 3.3.2 and 3.3.1

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 3 13:05:31 CEST 2007

The g_order tool requires a unique sort of index group.  There's lots of
discussion about it documented in the list archives.  In short, you need to use
make_ndx to generate an index file that contains _only_ groups pertaining to the
carbon atoms you want to analyze, separated by chain (i.e., sn1.ndx/sn2.ndx). 
Each atom type should be in a separate group.


Quoting ªL´­µ½ <d93543002 at ntu.edu.tw>:

> Hello, gmx developer and users:
>       After modifying the source code of g_order in GROMACS 3.3.1 with Bug
> #84 and compiling again, I got the error message when using g_order to
> calculate order parameteters of POPC bilayer.
>       The error message is : grp 1 does not have same number of elements as
> grp1.
>       Command line about generating .ndx file and using g_order are listed
> below :
>       make_ndx -f  XXX.pdb -o index.ndx              (XXX.pdb is the original
> structure of the system)  (I chose system or POP as my index group)
>       g_order  -f YYY.pdb -n index.ndx -s ZZZ.tpr -o -od
>        It will be gotten the same error message when using GROMACS 3.3.2
> version.
>        Is something wrong in my process ?
>        Thank you.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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