qmmm free energies

Guest -
	9:14:52 PM PDT - Thu, Jul 14th 2011 Hi, In qmmm free energy calculations, what is the meaning of ncycles in the qmmm directive. I am wondering how the ESP energy differences are averaged if more than one sampling cycles is used. For instance, if two sampling cycles are used, two free energy differences are obtained by the calculations. Which one should be used? Thank you Roy

Clicked A Few Times	10:26:35 AM PDT - Fri, Jul 15th 2011 The reason for introducing ncycles was simply to break free energy sampling into several stages. During each cycle -- Classical MD trajectory is generated for nsamples -- The resulting MD trajectory is then processed to generate free energy differences, current values are printed out, necessary information is saved to continue sampling The next cycle just builds up on the previous one, accumulating all the averages from the previous cycles. In that sense having N cycles with 1000 samples will lead to the same result as one cycle with N*1000 samples. If you system goes down case you can recover/continue simulations using information from N-1 cycle, but if N=1 you will loose everything.

Guest -
	10:15:25 PM PDT - Sat, Jul 16th 2011 Thank you for your reply. I have another question about xyzi files. In the online manual, it says "The xyzi is basically xyz structure file with an extra column that allows to map coordinates of QM atoms to the overall system" What do the "map coordinates" and the "overall system" mean here. For example of a trivial case that the xyzi and corresponding ESP files are same for A and B except that the xyzi files for A and B have a relative displacement or orientation. In such a case, can detalW(A->B) can be obtained. Thanks again.

Clicked A Few Times	5:38:27 PM PDT - Wed, Jul 20th 2011 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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