Dear all,
I studied the disassociation process of a ligand depart from an enzyme's active site by using the PMF method. The umbrella sampling and Weighted Histogram Analysis Method (WHAM) were used. However, when I used the WHAM to get final PMFs of this process, I found that the tolerance value, a parameter which specifies the convergence criteria of the WHAM calculation, influenced the free energy curve abnormally ( see the following figure).
In general sense, the smaller the tolerance, the more accurate the free energy will be. In my case, when tolerance was set to 0.1, the calculated binding free energy agreed with the experimental binding free energy quit well. However, when the tolerance became smaller, the deviation between calculated and experimental binding energy became larger, also the free energy curve became abnormal.
So could anyone give me some advice about the possible factors that may cause this phenomenon ?
Thanks in advance !
-Sun
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Received on Thu Dec 25 2014 - 20:00:02 PST
