Kukol, Andreas wrote:
Hi all,
When I look at the trajectory of a lipid/protein/water system generated with
Gromacs 4.05 on four cores, the lipid bilayer looks messed up with bonds drawn
all over the system, while the protein and water are displayed correctly.
This is similar to previous Gromacs3 trajectories that had been shuffled, but
not deshuffled before visualisation.
Did anyone see similar problems and is there a solution to display the lipid
correctly ?
Have you tried using trjconv to correct for periodicity effects? The frames of
trajectory files now contain "broken" molecules due to the implementation of DD,
so molecules (at the very least) have to be made whole. Usually trjconv -pbc
mol (or -pbc nojump) is the right way to start.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 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
