[gmx-users] Membrane simulation - error during EM after inflation step

Justin Lemkul jalemkul at vt.edu
Tue Feb 5 14:42:12 CET 2013

On 2/4/13 11:09 PM, John K wrote:
> Hello Justin,
> Thank you for providing a tutorial for membrane simulation.
> I am doing membrane simulation by following your tutorial.
> When I tried to do energy minimization after inflating the system i got the
> following result.
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  1.6157550e+17
> Maximum force     =            inf on atom 2093
> Norm of force     =            inf
> So the system is not converged well. I checked the output .gro file the
> protein came completely out of the bilayer.
> I tried to fix the problem by increasing the -fc value to 1000000 but still
> problem continues.
> Will you please tell me what will be the reason behind this problem and how
> to fix it.

If the protein is completely out of the bilayer, that means you haven't built 
the system properly.  EM will not cause massive displacement of any species, so 
a protein floating out in the middle of nowhere indicates it is incorrectly 
centered within the unit cell.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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