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<pre>><i> Maybe I don't fully understand your objective, but if you're just interested in <br></i>><i> secondary structure stability as a function of distance between two species, a <br></i>><i> slow steered MD run could accomplish that; you don't need umbrella sampling. If <br></i>><i> you're trying to get free energies associated with different configurations, <br></i>><i> however, then getting the PMF is a suitable method.<br></i><br>><i> -Justin<br></i><br>I'd like to be able to have a single peptide with the N-terminus anchored and pull the C-terminus with constant<br>velocity so that a force vs displacement plot could be generated.<br></pre> </body>
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