[gmx-users] Fatal error during lipid bilayer minimization

[Bharath K. Srikanth]

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.