Short answer is anything that has a B state parameter can be included in in Hamiltonian exchange.
If it's pull code or explicit restraints, it's controlled by restraint lambda. > I went through the manual and couldn't find any definite answers to the > following questions. > > First, I wonder if the reference positions of position restraints, not just > the force constants, of different replicas are exchanged in hamiltonian > exchange based on restraint-lambdas? For example, if I have 1 molecule that > has 2 structures, say, A and B and the following 2-component > restraint-lambdas: 1.0 1.0 with replica 0 starting in A and replica 1 in B, > would the exchange between replica 0 and 1 yield anything meaningful ? Right now, the pull code doesn't have B state positions, just force constants. It CAN be done using distance restraints, but then you have to make the atoms involved part of the same molecule. Adding B state distances to pull code was recently requested, and will probably be straightforward to put in soon. > In > other word, would the relaxation towards the other structure occur in both > states once an exchange was accepted? > > Another question is what types of restraints can restraint-lambdas act on? > For example, bond/angle/distance/position restraints, COM-pulling potential > ? Anything with a B state in gromacs topologies. -- 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
