Hi Omer, To check your periodicity use genconf:
genconf -f in.pdb -o out.pdb -nbox 2 2 2 Cheers, Tsjerk On Sun, Jun 21, 2009 at 11:23 AM, Omer Markovitch<[email protected]> wrote: > Dear All, > I would like to ask your help on the following - I want my simulation to > include a surface, and have PBC. > The surface I chose is aligned on the XY plane. However, the surface is not > a square. > The surface dimensions are a=b=169.2 & c=6.9 Angstroms, the angles are: > bc=ac=90 & ab=120 degrees. > > I have used "editconf -f -box 16.92 16.92 0.69 -angles 90.0 90.0 120.0". To > test this, I have used "trjconv -pbc nojump -center yes -boxcenter zero". My > problem is that the trjconv generates a structure where some of the surface > atoms are cut and/or overlapping... > > Could you please help me? Wheres the problem? > The input PDB I use is about 2 MB in size, so it can't be attached here. > > Koby Levy research group, > Weizmann Institute of Science. > http://www.weizmann.ac.il/sb/faculty_pages/Levy/ > > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.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 [email protected] http://lists.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
