Hi Hannes,
Many thanks for the reply. With regards to your final comment I understand conserving mass in theory, but I am a little confused regarding, "keep the mass-lambdas at one end-point as they can interact badly with constraints". I am testing pmx on a two-molecule one-system I.e., G-D2K-G and G-K2D-G in the same system. How ought I define the mass-lambdas for this system? (nothing accurate, just an example would be great)? Thanks Anthony On 01/06/2016 09:55, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Hannes Loeffler" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of hannes.loeff...@stfc.ac.uk> wrote: >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. -- 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.