Hi, Dejun- Right now, the vector of lambda parameters is simply vdw, coul, bonded, restraint, temperature. You can't have, say, 2 different coul vectors or two different restraint vectors for different restraints. But you can change any of these components.
You define the vector manually by writing out the list. So to do 2D in vdw and restraints, you would define states: vdw-lambdas = 0.0 0.0 0.0 0.5 0.5 0.5 1.0 1.0 1.0 restraint-lambdas = 0.0 0.5 1.0 0.0 0.5 1.0 0.0 0.5 1.0 Multidimensional movement in parameter space with replica exchange can be done with the md setting '-nex Nswaps'. This does multiple pair swaps, instead of just neighbor pair swaps. I'd suggest something like Nswaps = N^3, where N is the number of lambda states. This is a close approximation to Gibbs sampling (http://jcp.aip.org/resource/1/jcpsa6/v135/i19/p194110_s1), where _all_ permutations are selected based on their Boltzmann weight. It's an approximation because with a finite number of swaps, you don't quite get uncorrelated moves in state space, but it is rigorously correct thermodynamically. It is more powerful than randomly selecting a dimension to move in, since it allows moves in all dimensions simultaneously with proper weight. Note that the number of lambdas states is hardcoded as 1024, but that can (I think) be edited as desired without causing direct problems (other than perhaps needing to make the .mdp lines longer). We are working on more general multistate lambda vector formalism for 5.0. If you have suggestions, let me know. I'd be happy to look over input files or give additional advice on a specific setup. On Tue, Apr 2, 2013 at 12:52 PM, Dejun Lin <dejun....@gmail.com> wrote: > Hi Michael, > > Do the codes now support walking in multidimensional parameter space? i.e., > a state is defined by a set of lambda parameters {l1,l2,l3,...,ln} and a MC > move is attempted along one of the parameter, which is randomly picked. > > Thanks, > Dejun > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Hamiltonian-replica-exchange-umbrella-sampling-with-gmx-4-6-tp5006187p5006842.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
