[gmx-users] Clarity on TI free energy terms

[Nash, Anthony]

Dear all,

I¹m trying to understand the finesse behind the TI free energy in gromacs,
before taking it anywhere near a real production run, by running through
the FE methane in solvent tutorial and the thermodynamic cycles of small
peptides in the PMX paper. I roughly-understand a fair chunk, however, I
would appreciate some clarity on one or two points.

In the tutorial, charges are off in the topology and the electrostatic
coupling to lambda remains 0 throughout the 20 windows. I assume setting
col_lambdas=0 0 0 Š was for that very reason I.e., the charges were off?
Could the charges not have been left on and col_lambdas defined similar to
vdw_lambdas? 
(I understand that if charges remain constant, as vdw turns off, the
system will probably blow up as attraction brings molecules infinitely
close). 

If my transition is from a small molecule into a small molecule e.g.,
G-D-G to G-K-D, (the PMX paper) should I define all three lambdas:
vdw_lambdas, col_lambdas and bonds_lambdas? Between states A and B, VdW,
charges and bonds are all changing.

Many thanks
Anthony