Hello all,<br><br>I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system.<br><br>The command I am using is:<br><br> trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro<br>
<br>This runs without any error and ordered.gro is generated with random sequence of water molecules.<br><br>Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different "ordered" water molecules. <br>
I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the "ordered.gro" file.<br><br>What could be going wrong?<br><br><br>Thanks,<br>SN<br><br><br>