Dear Gromacs users,
I want to simulate a Cyclopentane (CP) system in Gromacs and I want to use TraPPE united atom force field. I first obtained the cyclopentane itp file using ATB server and now I want to change the parameters in that file to match the parameters mentioned in TraPPE-UA for CP. (http://trappe.oit.umn.edu/#UA)
I was able to change everything except for the parameters for 1-4 bonded interactions (dihedrals). To the best of my knowledge, TraPPE use Fourier dihedrals to calculate the U(torsion) and I have to translate it to Gromacs Ryckaert-Bellemans using the following formulas mentioned in Gromacs manual.
I took this approach and calculated the related constants for Ryckaert-Bellemans potentials for CP.
However, when I try to energy minimize my initial structure (made using packmol) with the modified topology file, I am not able to successfully energy minimize it and it says that the energy is very high.
What am I missing here?
Can someone help me to fix this?
Thanks for any possible help in advance.
Kav