[gmx-users] Fwd: The question from the tutorial: protein non-protein in .mdp file
tsjerkw at gmail.com
Thu Oct 30 08:32:54 CET 2008
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.
---------- 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>
First, this webpage is under construction.
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?
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.
> 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
3584 CH Utrecht
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