Hi Astrid, Besides all the useful advice regarding the visualization, note that the rhombic dodecahedron is smaller than the truncated octahedron and is more spherical, thus yields a more even distribution of water around your solvent, rendering an effect due to the box type less probable. In short, it's better to use a rhombic dodecahedron than a truncated octahedron.
Cheers, Tsjerk On 12/11/06, Hanna, Joanne <[EMAIL PROTECTED]> wrote:
Hi If you do: editconf -f box.gro -o box.pdb and view this in rasmol entering the command set unitcell on you should see the octahedral box. To view the octahedral box with the water you need to use the '-ur compact' option in trjconv. This should give you the octahedral representation. Jo -----Original Message----- From: [EMAIL PROTECTED] on behalf of Astrid Maaß Sent: Mon 11/12/2006 10:53 To: [email protected] Subject: [gmx-users] difficulties in creating octahedral boxes Dear all, I am new to gromacs and exercising, thus currently I am trying to follow the "Gromacs tutorial for Drug-Enzyme complex" of J. Kerrigan (many thanks) for my example molecule (alanine). I have used the sequence of commands below: pdb2gmx -f example.pdb -p ex.top -o ex_in.gro editconf -f ex_in.gro -d 1.0 -bt octahedron -c -o ex_in_box.gro genbox -cp ex_in_box.gro -cs -o ex_sol.gro -p ex.top genbox -cp ex_in_box.gro -cs -o ex_sol.pdb -p ex.top When viewing my system ex_sol.pdb with rasmol I notice that my alanine molecule is placed near to one face (inspite of -c) of a rectangular (inspite of -bt octahedron) box. editconf gives no warning and the final line in ex_in_box.gro seems to describe a non cubic box: 2.43930 2.29979 1.99168 0.00000 0.00000 0.81310 0.00000 -0.81310 1.14989 When filling the box with water molecules by use of genbox again no significant warning is given and the final line remains unaltered in ex_sol.gro. So why do I see my alanine in a cube of water molecules? I would appreciate any explanation or instruction how to create a non-cubic system very much. Thank you in advance! Kind regards, Astrid Maaß _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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://www.gromacs.org/mailman/listinfo/gmx-users 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
