Christian, PyMOL's default behavior is to pre-compute and cache molecular geometry in RAM. Although this provides optimal performance for small numbers of molecular states, due to RAM usage, it is an unworkable approach for viewing long MD simulations. So,
set defer_builds_mode, 3 before loading your trajectory in order to force PyMOL to only cache the current frame in RAM. In the current open-source build (and future builds 1.2+), you can also set defer_builds_mode, 5 to obtain VMD-like playback speed for lines, spheres, and nonbonded representations (immediate mode rendering -- geometry never touches RAM). Cheers, Warren -----Original Message----- From: Christian Seifert [mailto:cseif...@bph.ruhr-uni-bochum.de] Sent: Sunday, October 12, 2008 1:03 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] System freezes in cause of memory abuse Hi! I'm working with big structures and even bigger trajectories. When I try to load a trajectory, pymol takes the full 2GB RAM and freezes my PC (ubuntu 7.10/gnome/core 2 duo/2 GB RAM). The only way out is pulling the plug. :-( My Question: Is there a possibility to reduce the memory used by pymol? The "nice" command did not work, because it just reduces the available CPU time for pymol and not the available memory. Greetings Christian. -- M. Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: cseif...@bph.rub.de Web: http://www.bph.rub.de ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
