Thanks for the response, Justin. > Add a [constraints] directive for the molecule you want to make rigid and > use "constraints = none" in the .mdp file. Thus, only the bonds manually > set to be constraints will be constrained.
Great, this is a much better solution than the one I knew. > Note that by constraining one molecule but not another, you still can't save > any computing time, because the timestep of the simulation will still be > limited by any bonds that are still harmonic (especially X-H). Your system > probably won't be stable with dt > 1 fs, even with some molecule(s) > constrained. I don't wish to increase dt (since I have another flexible molecule to consider). I wish only to not have gromacs calculate forces for every atom of my macromolecule in the system, as I am not interested in its dynamics and it is important primarily as a steric exclusion volume for the flexible molecule. Will applying a an all-bonds constraint on the macromolecule reduce the computation time? > I don't see any value in constraining one molecule but not another. You > can't increase the timestep and you lose the ability to have rigid bonds. > The argument can be made that a rigid bond is a better representation of > reality than a harmonic one for most biological applications, or any done at > ambient temperature, really. My flexible protein is folding in the presence of a rigid macromolecule that restricts region that the flexible protein can occupy. I will be investigating whether the flexibility of the macromolecule is important later, though previous work by collaborators suggests not. I therefore do not wish waste computer time calculating forces on the macromolecule. > -Justin Thanks! Luke -- 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
