<chris.ne...@utoronto.ca> wrote: > If you simply want to know how to freeze one structure, then use freeze groups > and energy exclusions without pressure coupling, or use position restraints and > refcoordscaling=com with position restraints, or create an elastic network of > restraints.
Is it really not possible (or conducting to wrong results) to do NPT simulations with freeze groups? I did some tests with just a freeze group (a single molecule with no bonds with the rest of the system), and it caused a blow-up, indeed. But excluding all intramolecular interactions, for example using the "5" bond type and a large enough "nrexcl" value, or explicitly listing all exclusions in the topology, seemed to fix it. The coordinates of the frozen molecule do not change when the box grows or sinks... So, my conclusion was that NPT with a frozen molecule is possible, as long as no intramolecular terms are included. Am I wrong? Ignacio -- 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
