[gmx-users] Re,problem with EM

[Justin Lemkul]

On 11/20/12 1:04 PM, Ali Alizadeh wrote:
> Dear Justin
>
> Thank you for the quick reply
>
>> Dear All users
>>
>> I want my energy minimization of my system is converged to considered
>> value, when i do it,
>>
>> It is converged because it reachs to Fmax and i see this message :
>>
>> Steepest Descents converged to Fmax < 10 in 31702 steps
>> Potential Energy  = -1.6531438e+03
>> Maximum force     =  9.8014317e+00 on atom 162
>> Norm of force     =  2.9060462e+00
>>
>> my result:
>>
>> http://alichemical.persiangig.com/document/em.jpg
>>
>> When i represent profile of potential energy by g_energy, i can't see
>> my considered results,
>>
>> I should reach this result that this link is related to it,
>>
>> http://alichemical.persiangig.com/document/11.jpg
>>
>
>> That's right, I knew it but in your opinion, How can i get same
>> result, What's the value of emtol for my system?
>>
> Justin wrote:
>       If you want to reproduce the results of an MD trajectory, you
> need to be doing
>       MD, not EM.
>
>       -Justin
>
> I do not know my emtol value, How can i determine it?
>

emtol is simply a target value for the maximum force to reach during energy 
minimization.  I don't know that there is a terribly scientific way to determine 
what it should be, except for NMA calculations where it is particularly 
important.  The goal of EM is to achieve a reasonably stable system that is at 
an energy minimum and can be simulated further.

-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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