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Hello,
I’m trying to reproduce the IR spectra of water by using the Gromacs dipoles function to calculate the dipole autocorrelation, then performing the FFT of the autocorrleation. To do so, first I run the Gromacs dipoles function by executing the following line:
echo “0” | gmx_mpi dipoles -f prd.trr -s prd.tpr -o output_files/Mmol.xvg -corr mol -c output_files/dipcorr_mol.xvg
Then I take the dipcorr_mol file and perform the FFT. When I plot this, I see the IR peaks at the expected positions. However, I also see an offset of 0.5 of the signal (see plot)
Why do get this offset? Why isn’t the baseline of my signal centered at zero?
