GROMACS version: 2020.4
GROMACS modification: No
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Dear gromacs users,
I’m trying to calculate epsilon value of a peptide (frequency based).
So I am running 1ns NPT simulation of the peptide with PME, PBC, and epsilon_r=1 option in .mdp.
There is no solvents in the system and ions were added for charge neutral.
After the md production, I used ‘gmx dipoles’ and ‘gmx dielectric’ in sequence.
The options I used were
'gmx dipoles -corr mol -P 1 -temp 298
gmx dielectric -f epsilon.xvg (from gmx dipoles)’
I think the result after ‘gmx dielectric’ was weird. The epsilon(w) value was oscillating like sin/cos function.
Is something wrong with my simulation and the options?
And how can I obtain the imaginary value of the resultant epsilon?
I really need your help.