[gmx-users] trjorder not working

shivangi nangia shivangi.nangia at gmail.com
Thu Apr 28 20:08:12 CEST 2011

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?

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