Hi Lin, That tutorial doesn't really give a good procedure for production work simulations. Use a rhombic dodecahedron instead, with a distance to the wall (-d) of at least 1 nm. Maybe it's better to try the tutorial I put up on http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ It's not as good on the graphics, but the procedure is closer to what you need for proper simulations.
Cheers, Tsjerk On Sun, Sep 28, 2008 at 6:16 AM, Chih-Ying Lin <[EMAIL PROTECTED]> wrote: > > HI > I followed the tutorials > http://md.chem.rug.nl/education/mdcourse/MDpract.html > > the procedure is > 1. create the box > > Use a standard cubic box and be sure that the protein does not see its > images. This means that the distance from the the box wall should be greater > than half of the cut-off (1.4 nm) > > editconf -f minimized.gro -o minimized_box.gro -d 0.75 -bt cubic > > > 2. solvate the protein > genbox needs as input the protein in a box (minimized_box.gro) and a solvent > box (spc216.gro) and the topology of the solute (aki.top) and of the solvent > (spc.itp). > > genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p > aki.top > > Is it the same thing for the TIP4P-Ew water model? > > > Thank you > Lin > > > >> Then, I can say my system is under the water model-TIP4P-Ew. >> And, other simulation procedures are all the same for any kind of water >> model. > > What procedures do you mean? > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > -- 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 gmx-users@gromacs.org 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