Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > Quoting maria goranovic <[EMAIL PROTECTED]>: > > > Dear All > > > > I am running a 128-lipid bilayer simulation with standard parameters. The > > simulation abruptly crashed after 2 ns, and a look into the pdb files > > suggested that bonds were being broken and eventually the lipids explode. I > > tried increasing the cutoffs from 1.0 to 1.4, and this time also, the > > simulation exploded, but at a different time point.
And as an aside, broken bonds are only a visualization effect; mdrun doesn't write broken molecules. Also, providing your .mdp file would be of use. -Justin > > > > The energy remains nice and stable till the explosion. > > > > How does one fix this ? What is planting these bombs ? > > You'll have to describe how you minimized and equilibrated your bilayer > before > we'll have any idea what's going on. Also have a thorough look through the > archives; many users have posted about bilayers exploding (including yours > truly). > > -Justin > > > > > Thank you for suggestions. > > > > -- > > Maria G. > > Technical University of Denmark > > Copenhagen > > > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
