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? Thanks, SN
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