[gmx-users] g_lie and PME

Lei Zhou zhoumadison at gmail.com
Sat May 7 01:33:49 CEST 2005


I am trying to calculate the binding free energy of a ligand to a
protein, using g_lie based on two simulations (ligand in h2o and
ligand with protein). Someone mentioned that LIE is originally
developed with cutoffs, thus it is not necessary to put long range
energies (both coul and LJ) into consideration? And also what is the
most convenient way to calculate the long range Coul energy beteen
ligand and h2o, if necessary?

Is there a standard protocal for doing mdrun -rerun? Some people
suggested the following:
nslist=1; constaints=none; nstenergy=1. Are these setting necessary?

Thank you.

Lei Zhou

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