Hi, I am trying to perform expanded ensemble simulations between 2 states A (lambda=0) and B (lambda =1) with 6 intermediate lambda values.
In state B the Hamiltonian is rescaled, such that the epsilons of the vdW interactions, the charges, the bond, angle and dihedral constants are a multiple of the similar terms of State A. It's not quite clear to me (going through the archives of the gmx-users mailing list how to perform these calculations. One way to do this, is to use a single topology file in which the charges and the other terms are specified for both states A and B. However, it is not clear as to how should I scale the epsilons in the topology file. (My atoms are not mutated in state B. They are the same atoms with scaled epsilons.) Secondly, since I have the topology files for states A and B, is there a way I could perform the simulations (any particular way in grompp) where both the topology files can be preprocessed designating the end states and using the mdp options, the simulations corresponding to the intermediate lambda values performed?? -- 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
