[gmx-users] T-coupling: System vs. Protein Sol?

[David Mobley]

Flexibility is always desirable. For example, in free energy calculations,
sometimes one group (i.e. part of the protein, or a small molecule) is
decoupled or partly decoupled from the rest of the system. In this case it's
quite useful to be able to have a separate thermostat for the ligand or the
part of the protein, since it's not interacting with the rest of the system
(or partially noninteracting) and so there is actually no (or little) heat
transfer.  Presumably there are many other cases where you would want to do
this sort of thing.

David


On 2/15/06, David Mathog <mathog at caltech.edu> wrote:
>
> There are various predefined groups which may be specified in the
> tc-grps parameter file field.  The gmxdemo and speptide demos use
> "Protein Sol" and the other demos use "System".
>
> This is so not my field, but the members of the Protein and Sol
> groups are in intimate contact with each other so in the real world
> all of those elements would be in thermal equilibrium with each other.
>
> Why then use separate couplings to represent a protein system
> in Gromacs?
>
> Thanks,
>
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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