<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:10pt"><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt; "><span>Hello everyone,</span></div><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt; "><span><br></span></div><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt; "><span>I've used the rot+trans option in GROMACS trjconv to superimpose groups of atoms within a single molecular dynamics simulation. I am now interested in modeling a protein, and a rather thoroughly scrambled circular permutation of that same protein. I want to construct a superimposition which optimizes the alignment of selected residues within the two structures. But unlike in a standard trjconv superimposition, I will be trying to align atoms in one structure which correspond to atoms with different numbers in the other structure. So the
idea of groups as numbered atoms, as conventionally defined in a GROMACS .ndx file, would not seem to apply here.</span></div><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt; "><span><br></span></div><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt; "><span>Is this a practical task within GROMACS, or should I be looking elsewhere for the tool to accomplish the job?</span></div><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt; "><span><br></span></div><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt; "><span>Many thanks for your advice.</span></div><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt; "><br></div></div></body></html>