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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.