Dear Astrid, It seems as if the problem is in the presentation, not in GMX. trjconv -ur compact may help.
Ran. Astrid Maaß wrote: > 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 > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ 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
