Ragothaman Yennamalli wrote:
Dear all,
In a particular setup of a protein interacting with
ions, the protein needs to be simulated without ions
and after a certain point of time the ions are
introduced to the system, so as to check of the
protein undergoes refolding in the presence ions or
not. Since it is a known fact that in the absence of
ions protein undergoes conformational change and in
the presence of ions the protein remains stable.
It's not possible for there to be an "absence of ions" in a physical
system. Charge separation is too expensive.
My question is: Can two different distance cutoffs be
defined in gromacs? for eg The distance range for
protein and ions not more than 20Angstroms and for
solvent-solvent not more than 8Angstroms.
No. This is not implemented, not easy to implement, and would likely
require a force field to be re-parameterized for it.
Mark
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