Date: Wed Jul 18 2012 - 07:18:10 CDT
We are working currently in some free energy calculations on a protein DNA complex using unbrella sampling with the minimal distance between the two molecules as the reaction coordinate. Everything goes OK except that the last base pair in the DNA opens from time to time and contacts the protein. We would like to restrain it in order to maintain the watson-crick pairing but we don't know if it would do any harm to the PMF. As we are using tcl forces we know exactly how much energy the bias is applying to the system so in principle the should be no mixing between the pulling restraint and the bais pairing restraint.
We were then wondering if somebody can point to anything against this approach. Also, i am not sure now if we need to use only the bias energy for the unbrella restraint or it is better to add the ones from the bases restraint in order to do the histograming as well. In principle, i think you need to add all the extra energy added to obtain every particular microstate, but i am not sure.
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