Re: [gmx-users] Periodic Boundary Condition Issues
Try combining indices with that, use make_ndx -h. --Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Wed, Jul 22, 2009 at 18:27, Justin A. Lemkul jalem...@vt.edu wrote: The trjconv -pbc options were designed to fix this sort of issue. ___ gmx-users mailing listgmx-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
[gmx-users] Periodic Boundary Condition Issues
Hello, I am trying to analyze the trajectory of the estrogen receptor alpha in water. As you know, the ER is a dimer and as such when it approaches the boundary for the simulation one of the monomers jumps to the other side of my box and thus screws up any post simulation calculations that we are interested in, especially since the focus of our project is the dimerization interface. Is there any way to fix this so that visually the dimer doesn't appear to split? Thanks, David ___ gmx-users mailing listgmx-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
Re: [gmx-users] Periodic Boundary Condition Issues
Cooper, David R wrote: Hello, I am trying to analyze the trajectory of the estrogen receptor alpha in water. As you know, the ER is a dimer and as such when it approaches the boundary for the simulation one of the monomers jumps to the other side of my box and thus screws up any post simulation calculations that we are interested in, especially since the focus of our project is the dimerization interface. Is there any way to fix this so that visually the dimer doesn’t appear to split? The trjconv -pbc options were designed to fix this sort of issue. Dimers and complexes can be a bit tricky, so you'll have to play around with different options to find the one that works for you. -Justin Thanks, David ___ gmx-users mailing listgmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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
