[gmx-users] ordering components of system using trjorder

shivangi nangia shivangi.nangia at gmail.com
Thu Apr 28 18:54:39 CEST 2011

Dear gmx-users,

I wish to order the components of my system with respect to the polypeptide
using trjorder.

I want to select my first group as the protein and the second group to be
ordered is non-protein (i.e all other components in the system except

the command I am using is:

trjorder -f shape.gro -s shape.tpr -da 0  -o ordered.gro

The problem is -na "int" is required, but the rest of my system contains
TIP4P water, methanol, Li ions so the na is different for all non-protein

Is there a way to override option -na and still get non-protein part of the
system ordered with respect to the polypeptide (protein)

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