| 5:38:27 PM PDT - Wed, Jul 20th 2011 |
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Overall system means just that overall system, e.g. protein consisting of number of residues, etc.
In the free energy simulations we modify part of the system by means of xyzi and esp files. The plain xyz file has no notion of residues just atom names, and without that extra column of information it would be impossible to know which atom should be modified. Free energy difference can be obtained for any combination of coordinate/charge changes between A and B configurations, including those where only coordinates (or charges ) are changed.
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