[gmx-users] trjorder not working

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 29 03:43:42 CEST 2011

On 4/29/2011 11:29 AM, shivangi nangia wrote:
> Hello,
> The manual explaining trjorder says:
> trjorder orders molecules according to the smallest distance to atoms 
> in a reference group or on z-coordinate (with option -z). With 
> distance ordering, it will ask for a group of reference atoms and a 
> group of molecules. For each frame of the trajectory the selected 
> molecules will be reordered according to the shortest distance between 
> atom number -da in the molecule and all the atoms in the reference 
> group. *The center of mass of the molecules can be used instead of a 
> reference atom by setting -da to 0*
> In order to arrange water molecules in accordance with the COM of the 
> polypeptide, I chose -da 0.

As it says above, -da refers to an atom or COM of the molecule, not the 
reference group. This could be worded better in the documentation.

Be sure you're choosing the groups you think you are choosing - you not 
copying relevant parts of your terminal output into emails is making 
things difficult.


> Am I wrong?
> Thanks,
> SN
> On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 4/29/2011 4:08 AM, shivangi nangia wrote:
>         Hello all,
>         I am trying to order the TIP4P water molecules in my system
>         with respect to the polypeptide in my system.
>         The command I am using is:
>          trjorder -f shape.gro -s shape.tpr -da 0  -na 4 -o ordered.gro
>         This runs without any error and ordered.gro is generated with
>         random sequence of water molecules.
>         Just to cross check I calculated the distances between one of
>         atoms of the polypeptide and oxyegn atom of different
>         "ordered" water molecules.
>         I found, there is no ascendig trend in the distances with
>         respect to the polypeptide as a go down in the "ordered.gro" file.
>         What could be going wrong?
>     -da 0 has a particular effect - is it appropriate? Did you choose
>     the right groups? You could use the -nshell option to probe what
>     trjorder thinks is going on.
>     Mark
>     -- 
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