[gmx-users] New parameter for boron

Hernan Ahumada hernan at chem.gla.ac.uk
Mon May 30 18:06:48 CEST 2011

I am trying to implement parameters for boron because I am simulating a
carborane (cluster molecules of CH and BH units). This corresponds to a plastic
crystal phase and the shape is a icosahedra cage. In this kind of phase, the
molecules are arranged within a lattice, but they do not have restriction in
the reorientational motion. Besides, they have correlation time in ps second. I
found these parameters for boron(J. Chem. Phys., Vol. 105, No. 6, 8 August 1996)
and I simulate 100ns of this lattice. I also calculated the relaxation time, and
they reproduce the experimental results. The problem is the energy, because the
potential energy is positive.
How can I explain the positive values for the potential energy? Do you think the
problem is in the bond an angle force constant?

Energy                      Average   Err.Est.       RMSD  Tot-Drift
Bond                        7447.87          6    131.939    33.4159  (kJ/mol)
Angle                       31032.8        5.2    143.546    35.5282  (kJ/mol)
LJ-14                       7099.96        0.1    13.6658    0.68167  (kJ/mol)
Coulomb-14                  21583.6       0.79    14.3526    4.48213  (kJ/mol)
LJ (SR)                    -11617.4         68    162.056   -426.317  (kJ/mol)
LJ (LR)                    -984.104        4.5    10.6753   -27.9057  (kJ/mol)
Coulomb (SR)               -56.6116        5.6    20.1478   -29.6642  (kJ/mol)
Coul. recip.                1529.99         11    27.2492   -60.9081  (kJ/mol)
Potential                   56036.1         77    273.483   -470.687  (kJ/mol)


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