[gmx-users] Fatal error during lipid bilayer minimization

[Mark Abraham]

On 13/09/2012 4:33 PM, Bharath K. Srikanth wrote:
> 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?

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Mark