<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hi,</div><div> I was using gromacs 4.0.7 to calculate the scattering intensity of polymer solvated in a solvent. But, I found a discrepancy in the normalization of the calculation when considering only a subset</div><div> of the entire system ( e.g . only solute from the entire solution) :</div><div>This is what I found:</div><div><br></div><div> I first tried to calculate the scattering intensity of *only* the polymer ( i.e the solute) using trajectory file of the entire solution and .tpr file of the entire solution using an index file as shown below</div><div><br></div><div><div>g_rdf_4mpi -s topol -f traj -noxvgr -n -sq sq_polymer_only << EOF</div><div> 6</div><div> EOF</div></div><div>( Here index-group 6 is the entire polymer).</div><div><br></div><div>But,
then I generated a .tpr file *only* for the solute ( i.e no solvent) and used trjconv to generate the .xtc file *only* for the solute </div><div><br></div><div>trjconv_4mpi -s topol.tpr -f traj.xtc -n index.ndx -o traj_polymer_only.xtc<br></div><div><br></div><div>Now, If I try to calculate the scattering intensity, this time using newly generated .xtc file *only* containing the solute and the new .tpr file *only* containing the solute as follows:</div><div>g_rdf_4mpi -s topol_polymer_only.tpr -f traj_polymer_only.xtc -noxvgr -sq sq_polymer_only1 <br></div><div><br></div><div>I get much higher scattering intensity compared to the earlier case ( where trajectory of the entire solution was used and a index file was provided to consider the solute only for calculation purpose), however the peak position is same for both cases. I think, possibly, there might be a bug which does the normalization for the entire solution in
stead of the subset of the system if asked to. </div><div>Any help in clarifying it will be helpful.</div><div><br></div><div><br></div><div>Sanku</div></div></body></html>