[gmx-users] Calculating the dielectric constant of a ligand

[Sajad Ahrari]

Dear Users,
I am trying to calculate the dielectric constant of a ligand (5RC), so that I can use the output number in the binding free energy calculations by MM/PBSA method (by g_mmpbsa package). For this purpose, I used the "gmx_mpi dipoles -s 5RC.tpr -f 5RC_last20ns.xtc -corr mol  -c dipcorr.xvg" command to produce the dipcorr.xvg and the used it as the input in "gmx_mpi dielecteric -f dipcorr.xvg -d deriv.xvg -o epsw.xvg -c cole.xvg" command. I suspect that the epsw.xvg should contain the desired information. However, I am not sure how to interpret it. Could you please give me a clue on how to proceed? The outputs are attached.
Thank you