Think outside of the box when using Periodic Boundary Conditions. :p
Tsjerk On Wed, Jul 15, 2009 at 9:14 AM, Mark Abraham<mark.abra...@anu.edu.au> wrote: > nikhil damle wrote: >> >> Hello, >> >> When I am running energy minimisation of protein-peptide complex, >> minimised structure shows a space for the protein in water box; but peptide >> remains inside the box while protein is seen outside. >> >> Same occurs when I keep pbc = xyz and/or nstcomm = 1 >> >> in ..top file, I am including individual posre.itp files (posre_A.itp and >> posre_B.itp) separately. >> >> How should I fix this problem ? > > See this page, in particular the bottom. > http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions > > Mark > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > 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 gmx-users-requ...@gromacs.org. > 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
