On Wed, 1 Jun 2016 07:54:56 +0000 "Nash, Anthony" <a.n...@ucl.ac.uk> wrote:
> 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). Technically, Gromacs allows you to vary both vdW and Coulomb lambdas simultaneously because Gromacs can apply softcore potentials to both. In practice though it seems that many workers still prefer to separate the two terms from each other. > 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. Lambda paths are only about separating the various force field terms from each other. If you do not explicitly state any of those lambda vectors they will adopt they same lambdas as specified in fep-lambdas, see manual. I do not see a reason why you would want to separate out the bonded terms as well. They are subject to a linear transformation only anyway. What you may want to do is to keep the mass-lambdas at one end-point as they can interact badly with constraints. In a proper thermodynamic cycle mass contributions must perfectly cancel. Cheers, Hannes. -- 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.