[gmx-users] protein simulation

[elham tazikeh]

Dear GMX users
i want to compare binding free energy between experimental and MD
computations
In experimental methods, we assumed that all atoms of a protein that
binding to ligand, butin MD simulations, we just assume the sections of
subdomain(s) that binds to ligand

Is this way correct to comparing the binding free energy have got from MD
with experimental analysis?

or in MD simulations, we must simulate all of subdomains in a protein
whatever bind to a ligand or not?

finally, suppose that there are for example 2 molecules of a ligand in a
pdb file of a protein (for instance in pdb:2i30 there are 2 molecules of SAL
we must suppose all of two molecules in pdb file or
once, simulate protein with ligand1 (SAL1) and after that simulate with
ligand 2 (SAL 2)?

Regards