[gmx-users] Checking interaction energies - regd

ramesh cheerla rameshgromacs at gmail.com
Mon Jun 18 14:21:49 CEST 2012

Dear Gromacs users,

                                  I am using buckingham potential in my
simulations for that  I have copied charmm27.ff  to my working directory,
and have modified it, to know whether it is working  properly or not, I
have run one step simulations and checked the energies obtained in
simulations with the energies obtained in the programs that I have written
to calculate these energies,
In this case non-bonded and dihedral  energies are matching perfectly,
and   am getting a difference of  bond stretching energy 1.74 Kj/mol  per
bond and a large variation in bending energies i.e 56.4 kj/mol per angle,
for bending i have used function type 1  and included same functional form
i.e  0.5*Ktheta*(theta-theta0)^2 in my program and I have used all the
units according to Gromacs conventions in my programs.
Can anyone please explain the reason for difference.

Thank you in advance.

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