[gmx-users] trjorder not working

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 29 02:29:18 CEST 2011

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.


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