[gmx-users] LIE method

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Sat Jan 11 08:10:48 CET 2014

hi dear GMX users
I simulated protein-ligand complex for 20 nanoseconds. I want to calculate free energy by LIE method so I simulated ligand in water in the same conditions. I used PME and full periodic boundary conditions in my simulations so I wrote a new .mdp file that didn't use PME (I used cut off) and used following command for protein-ligand complex simulation:
mdrun -s newtpr.tpr -rerun full20ns.xtc
then I extract -Elj and -Eqq of ligand in water simulation and use g_lie command.
are these steps sufficient. is the stage or another commandnecessary?
Thanks and best wishes

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