[gmx-users] possible bug in structure factor calculation in g_rdf?
msanku65 at yahoo.com
Fri Aug 12 18:33:38 CEST 2011
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
of the entire system ( e.g . only solute from the entire solution) :
This is what I found:
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
g_rdf_4mpi -s topol -f traj -noxvgr -n -sq sq_polymer_only << EOF
( Here index-group 6 is the entire polymer).
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
trjconv_4mpi -s topol.tpr -f traj.xtc -n index.ndx -o traj_polymer_only.xtc
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:
g_rdf_4mpi -s topol_polymer_only.tpr -f traj_polymer_only.xtc -noxvgr -sq sq_polymer_only1
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.
Any help in clarifying it will be helpful.
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