[gmx-users] Water molecule starting at atom 5113 can not be settled.

[Justin Lemkul]

On 11/6/12 2:10 PM, Ali Alizadeh wrote:
> Dear Justin
>
>      >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?
>
> Yes, But i got a lot of errors in my md run,
>
> in your opinion, how can i solve this error?
>
> I reduced my dt,
>
> My system is biphasic(water and methane and propane and methane in 300
> bar and 240 k, ff is gromos45a3)
>

If mdrun fails to converge, then you shouldn't proceed to MD, since the system 
is not at a stable minimum.  The most common cause of EM failing is bad atomic 
clashes, which means you need more careful system preparation or more delicate 
minimization.

-Justin

>
>> 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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