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

[Justin Lemkul]

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

-- 
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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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