Dear all
I want to calculate the free energy difference between QM/MM Hamiltonian and MM Hamiltonian for an acetamide molecule soaked in periodic boxes of TIP3P waters. For the QM/MM simulation, the QM region is the solute molecule acetamide and the MM region is water. The QM method used in the QM/MM simulation is BLYP/6-31g* .
I use SANDER module with option imin=5 to calculate the potential energy of each step of the QM/MM MD (with the same parmtop and imaged crd )。 The input file of imin=5 and QM/MM were attached.
My quetions are:
1, The potential energy of the same snapshot given by QM/MM MD (which can be read in the output file) is different to that calculated by SANDER with imin=5, the energy of QM region is almost the same, but the other items have large difference especially for the BOND term. I want to know why?
2, I also want to know whether the potential energy printed in the out file of QM/MM MD is the total potential energy of the system or not? Any scale or missing terms used here ?
3, Is the vdW term printed in QM/MM MD out file is the sum of the vdW interaction energy among the solvent molecules and that between QM and MM region?
4. Is the ELE item printed in QM/MM MD out file only include the electrostatic interaction between QM and MM region?
--
mt wang
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- application/octet-stream attachment: imin_5.in
Received on Mon Apr 25 2016 - 02:00:05 PDT
