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On 4/27/2011 3:16 PM, Mr Bernard Ramos wrote:
<blockquote cite="mid:500096.37873.qm@web161516.mail.bf1.yahoo.com"
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<div>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.</div>
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<div>Thanks,</div>
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<div>Bernard</div>
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<br>
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.<br>
<br>
Mark<br>
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