[gmx-users] LIE method

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Fri May 30 13:54:00 CEST 2014

dear justin
A few months ago I asked you a question about LIE method. 
 to your guide, i wrote a new .mdp file that didn't use PME (I used RF) 
and used following command for protein-ligand complex? and ligand-sol 
?mdrun -s newtpr.tpr -rerun full20ns.xtc
?then I extract -Elj and -Eqq of ligand in water simulation and use g_lie command.
But the obtained free energy has great difference with the experimental value.

 told me that i must re-calculate energies from? PME systems, then i 
must take the difference of the energies from another system where the 
same correction hasn't been applied.
Please explain this. How do I do it?
I have urgent need to calculate the free energy.
Thank you sincerely

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