[gmx-users] free energy calculation.

[neelam wafa]

Hi!
Dear gmx users,
I have md simmulations of a protein with four different ligands. now I want
to calculate the free energy of binding. which method does suit after md
simmulation?  either g_mmpbsa or gmx BAR  method.  If I use BAR method is
it necessary to set charges to zero as in the tutorial given at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html.

I s necessary to turn off couloumb interactions for calculating free energy
of ligand protein complex. if i want to use coloumb interactions also then
should i set the

coul_lambdas values in the same way as vdw_lambdas.

Another question is that there is another tutorial available at
http://www.gromacs.org/@api/deki/files/262/=gromacs-free-energy-tutorial.pdf

In this tutorial the system has been equilliberated before generating
the lambda states.

while in the justin tutorial each lambda state is equiliberated separately.

kindly tell me which one is more suitable for a protein ligand complex.

looking forward for your cooperation.

sorry if the questions are trivial.

Regards

Neelam

Ph.D scholar