[gmx-users] EM and an error: Water molecule starting at atom 5113 can not be settled.

Justin Lemkul jalemkul at vt.edu
Tue Nov 6 19:56:15 CET 2012

On 11/6/12 1:37 PM, Ali Alizadeh wrote:
> Dear All users
> 1- I got an error when i wanted to perform EM,  my emtol = 100 but it
> did not converge
>   Water molecule starting at atom 5113 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> ...
> I saw the pdb files and understood what did the happen,
> For solving this error, so i want to perform EM with emtol=1000

What did you do to fix the problem?

> it converged,  in next step i got em.gro as a input file and perform
> another EM with emtol=900
> It converged , and i continued to emtol=100

Did it work the second time?

> Is my method true?  I do not know my energy profile(i got by this
> method)  is correct,
> 2- Does this parameter affect on my md production? (when i use
> emtol=1000 or emtol=100)

The tolerance setting the desired value of Fmax.  If the EM algorithm reaches a 
force below the tolerance, it finishes.  Without knowing what your system is or 
what you intend to do, it's impossible to state what level of emtol is sufficient.



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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