[gmx-users] Urey-Bradley constant in CHARMM to GMX

[Mark Abraham]

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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