[gmx-users] trjorder not working
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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