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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
