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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