[gmx-users] Re, problem with EM

[Justin Lemkul]

On 11/20/12 12:17 PM, Ali Alizadeh wrote:
> Dear Justin
>
> Thank you for your reply,
>
>>
>> 1- In the first plot, unit of y axis is kj/mol, and you said above i
>> should use -nmol, i  confused, Why is the unit of y axis kj/mol
>> without using -nmol?
>>
>
>           Because that's the energy unit Gromacs always uses.  The
> energy given is kJ per
>           mole of equivalent systems.  In the second plot shown above,
> the magnitude of
>           the energy suggests kJ per mole of individual molecules.
>
> I understood,
>
>
>> 2- I want do EM so that energy of my system reaches to considered
>> value, but i never reach it exactly, what's wrong?
>>
>
>            You set an EM tolerance of 10 kJ/(mol-nm), which is a force,
> and mdrun achieved
>             that.  You can't ask an EM algorithm to produce the same
> result as a long-time
>             MD run, as is shown above.
>
>             -Justin
>
> 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?
>

If you want to reproduce the results of an MD trajectory, you need to be doing 
MD, not EM.

-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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