Thanks for your response, Chris. > If I read between the lines correctly, you know how to do this in gromacs, > but you wish that you got a big speedup from freezing most of the atoms in > your system.
Partly; the only method I knew of was inelegant and likely to cause bizarre outcomes. >If that is the case, then I think that gromacs can not help you > in its current form. Therefore, I suggest that you try the Charmm software. > It may be slower overall, but it gives you the speedup you expect when you > freeze 95% of the atoms in your system so it may be much faster for your > usage. Other software may also do this, but I have no experience with it. If > you have explicit water, this won't be of much use since you're still only > freezing <10% of the atoms in your system. I am using an implicit solvent, and the macromolecule I wish to hold rigid accounts for >99% of the atoms in my system. Additional extensions I later wish to employ are available only for gromacs, so charmm is not an option for me. > 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. Great; I will look into this. > Chris. 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
