On Wed, 1 Jun 2016 12:06:20 +0000 "Nash, Anthony" <[email protected]> wrote:
> vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 > 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 > mass_lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 > 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 > fep_lambdas = 0.0 0.1 0.1 0.2 0.2 0.3 0.3 0.4 0.4 0.5 0.5 0.6 0.6 > 0.7 0.7 0.8 0.8 0.9 0.9 1.0 1.0 This will transform both vdW _and_ Coulomb terms at the same time but at a different pace. Maybe you want something like fep-lambdas = 0.0 0.2 0.4 0.6 0.8 1.0 1.0 1.0 etc. vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.10 etc. mass-lambdas as above This will first transform Coulomb and bonded terms in the first six lambdas and vdW from the 7th lambda onwards. This also assumes that you have vanishing atoms only. If you have appearing atoms only you would obviously have to revers the order, and when you have both you will have to run with two mdp/tpr setups. > couple-moltype = protein > couple-lambda0 = vdw-q > couple-lambda1 = vdw-q This will decouple all atoms in the 'protein' selection from the environment. This is for absolute transformation and not what you seem to want to do i.e. a relative transformation of one residue into another. So avoid those parameters. -- 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 [email protected].
