[gmx-users] query about diferent cutoffs

[Mark Abraham]

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