[gmx-users] simulation settings

[Mark Abraham]

On 1/03/2010 12:00 AM, politr at fh.huji.ac.il wrote:
> Dear Gromacs users and developers,
> I want to perform simulation of peptide dissolved in water using NPT.
> For constant temperature I use Berendsen temperature coupling. Do I have
> to define tc-grps for 2 groups (protein and solvent) or I may use
> tc-grps =System.
> What is the difference? The person who introduced gromacs to me uses
> tc-grps = Protein Sol_Ions
> but he is not sure why it should be in this way if at all
> Can you, please elucidate this issue to me.

There's some quick advice here 
http://www.gromacs.org/Documentation/Terminology/Thermostats, otherwise 
consult some textbook material.

Mark