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
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
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
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
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
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
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
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