[gmx-users] Fwd: The question from the tutorial: protein non-protein in .mdp file

[Tsjerk Wassenaar]

Hi Lin,

Better keep this discussion on the list now.

Sorry about the link. Got screwed up. It should only consist of the
first part: http://wiki.gromacs.org/index.php/Thermostats
Then, if you don't have protein in the first place, you can't rely on
standard groups. You'll have to work with an index file to make the
distinction. Also, I don't know how large your solute/system is. In
some cases it may be better to use a single group "System", which is a
standard group (available without supplying an index file).

In any case, DON'T couple each molecule separately.

Cheers,

Tsjerk


---------- Forwarded message ----------
From: Chih-Ying Lin <chihying2008 at gmail.com>
Date: Thu, Oct 30, 2008 at 8:20 AM
Subject: Re: The question from the tutorial: protein non-protein in .mdp file
To: Tsjerk Wassenaar <tsjerkw at gmail.com>


HI
First, this webpage is under construction.
http://wiki.gromacs.org/index.php/ThermostatsNon-Protein


Second, how about a system with NO proteins.
The system includes A molecules, ions, and water.

May I set two groups - A_molecule and non-A_molecule  ???
Or, I have to treat each molecule differently?

Thank you
Lin





On 10/30/08, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Lin,
>
>  Please read http://wiki.gromacs.org/index.php/Thermostats
>  Non-Protein obviously includes everything that is not protein, such as
>  solvent, lipids, ligands and ions. You can be more confident about
>  your reading ability. In more complex systems, it may be necessary to
>  spend a bit more time thinking about this, as a ligand, cofactor or
>  bound ion may be better of treated as part of the protein.
>
>  This one I bounce to the Gromacs list as it is better off there
>  (related to Gromacs more than to the tutorial), and will be archived.
>
>  Cheers,
>
>  Tsjerk
>
>
>  On Thu, Oct 30, 2008 at 6:42 AM, Chih-Ying Lin <chihying2008 at gmail.com> wrote:
>  > Hi
>  > In the system of the tutorials, there are proteins, water, Na+, Cl-.
>  >
>  > In the .mdp files, there are two categories, protein and non-protein.
>  > I suppose that water, Na+, Cl- are in the group of non-protein.
>  > Am I right? or, non-protein only =water?
>  >
>  > Later on, I will simulate a system with protein, another molecule,
>  > water, and ions.
>  > Could I just categorize them with protein and non-protein?
>  > And, non-protein = another molecule, water, and ions????
>  > Will the thing go in that way?
>  >
>  >
>  > Thank you
>  > Lin
>  >
>
>
>
>
> --
>  Tsjerk A. Wassenaar, Ph.D.
>  Junior UD (post-doc)
>  Biomolecular NMR, Bijvoet Center
>  Utrecht University
>  Padualaan 8
>  3584 CH Utrecht
>  The Netherlands
>  P: +31-30-2539931
>  F: +31-30-2537623
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623