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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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