[gmx-users] about free energy calculation by LIE method

mircial at sjtu.edu.cn mircial at sjtu.edu.cn
Wed Jul 8 15:20:39 CEST 2009

Dear All:

        I want do some free energy calculation by  LIE method.  I read  
the "GROMACS Tutorial for Drug ? Enzyme Complex" carefully and know  
the method in gromacs to do free energy calculatin by LIE method.  
However I found the following words at the end of the tutorial:  "In  
this tutorial, we used PME and full periodic boundary conditions.  
Performing LIE computations with PME requires additional work to  
account for the longrange contribution. This takes a lot of work! We  
recommend using NVT ensemble using a water shell with cutoffs or Shift."

       Does anyone can tell me what additional work do  I need to do  
if I want to calculate free energy by LIE method when I used PME in my  
simulation. Or, dose anyone know how to using a water shell in gromacs  
simulation, inorder to do free energy calculation by LIE method in a  
right way?

      Thank you in advance.

                                            R-X  Gu

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