Hi I am trying to simulate the self-assembly of course-grained DSPC lipids into a lipid bilayer. I made a box (7.5 x 7.5 x 7.5) containing 128 DSPC lipids, and added 768 molecules of water to the system, and ran a minimization (using em.mdp). The summary of the results is below.
Reached the maximum number of steps before reaching Fmax < 10 writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 501 steps. Potential Energy = -4.2206562e+04 Maximum force = 4.0814236e+02 on atom 197 Norm of force = 1.2755975e+01 gcq#88: "I Don't Want to Catch Anybody Not Drinking." (Monty Python) I also did further minimisations, reducing the max. force to about 29, and the norm of force to about 1.96 For the next step i.e bilayer self-assembly, I ran another minimization (using md.mdp) and I received the following fatal error: Program mdrun, VERSION 4.5.5 Source code file: domdec_top.c, line: 356 Fatal error: 1 of the 2944 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck How should I deal with this? Thanks. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
