[gmx-users] Rigid structure and flexible structure present in sing system

Hi, For a while I've been looking for a way to include a rigid (macromolecular) structure and a flexible (small-protein) structure in a single system and have not had much success. I looked for a way to apply a different set of constraints to each structure, but couldn't find one. I looked into m

[gmx-users] Rigid structure and flexible structure present in sing system

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. 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 Charm

Re: [gmx-users] Rigid structure and flexible structure present in sing system

Luke Goodsell wrote: Hi, For a while I've been looking for a way to include a rigid (macromolecular) structure and a flexible (small-protein) structure in a single system and have not had much success. I looked for a way to apply a different set of constraints to each structure, but couldn't

Re: [gmx-users] Rigid structure and flexible structure present in sing system

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

Re: [gmx-users] Rigid structure and flexible structure present in sing system

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

Re: [gmx-users] Rigid structure and flexible structure present in sing system

Luke Goodsell wrote: 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

Re: [gmx-users] Rigid structure and flexible structure present in sing system

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 c