You can play with mdrun_hole (search the site) which is designed to create a protein-shaped hole in a lipid simulation (also making a hole in the water). I'd probably just delete the offending waters, and reequilibrate, myself.
----- Original Message ---- From: N-J.M. Macaluso <[EMAIL PROTECTED]> To: [email protected] Sent: Tuesday, November 6, 2007 2:11:47 PM Subject: [gmx-users] problem with waters in protein/membrane simulation Hello, I'm having a small but significant problem with simulating a protein inserted in a DPPC membrane. I have simulated the system for 15 ns with position restraints on the protein to allow the lipids to anneal around it, but have recently found a small problem. I found a small gap between the protein and lipid where some water molecules embedded themselves. Is there any way I can change the parameters of the simulation to remove these waters, so that the lipids will aggregate properly around the protein? What would the best solution be? Should I just remove these waters manually? Thanks, Max Macaluso _______________________________________________ gmx-users mailing list [email protected] http://www.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 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list [email protected] http://www.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
