Force Field Parameters and Accuracy

In a MD simulation with no experimental restraints, any results depend critically on the details of the force field and the simulation parameters. If one is refining with respect to an extensive NMR data set, then presumably the experimental data are the most important factor determining the final structures. 

A more difficult question is the relative balance between the conventional force field and the pseudo-energy terms representing experimental data.81 If 

When making such a decision, some considerations should be borne in mind. First, if one is using a refinement scheme that produces a known distribution of structures, then one can calculate the likely deviation that the pseudo-energy terms will permit. For example, if an MD refinement is used, structures will be able to cross barriers of about BT. Then, if one is using a quadratic form to enforce distance restraints, one could recast Eq. [9] as follows to get an idea of the violations that would be permitted for a given force constant and temperature  

Another important effect of pseudo-energy force constants is controlling the distribution of errors. For example, a misassigned NOE may show up as a residual violation if a small value for Kdc is used, but it may cause a distortion of the structure and high potential energy if Kdc is large. 

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