On 4/27/2011 3:16 PM, Mr Bernard Ramos wrote:
The Urey Bradley constant in CHARMM is expressed in units of kcal per
(mol squared angstrom). However, in the Gromacs manual in Table 5.5,
it is expressed in kJ/mol. How do we convert the constant from kcal
per (mol squared angstrom) to kJ/mol in gromacs. Could gromacs have
been expressing this constant in kJ per (mol squared nanometers)
rather than in kJ/mol.
Thanks,
Bernard
Yes, the dimensions in the table have been wrong for years. The units of
k_UB are kJ mol^-1 nm^-2, as one would expect from eq 4.55 in section
4.2.7. Internally, the function that implements the 1-3 harmonic
distance penalty is implemented using the same function as all the other
harmonic functions - no funny business.
Mark
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