Hi,
I have ran several simulations between large proteins and would like to calculate the relative free energy of binding (ΔΔGbind). I usually use MMPBSA for shorter simulations, but now when I try that for these larger ones, there is a RAM issue on my computer. Is there a way using GROMACS to calculate that as well as the contributions of specific amino acids?
I see on the GROMACS tutorial the LJ and Coul energies are mentioned. Are those of use for me?
I would greatly appreciate any help.
Thank you in advance,
Isaac