[gmx-users] Energy minimization

[Kieu Thu Nguyen]

Thank Justin so much !


On Sat, Feb 23, 2013 at 1:50 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/21/13 9:10 PM, Kieu Thu Nguyen wrote:
>
>> Dear all,
>>
>> I can not distinguish when the Fmax < 10 kJmol-1nm-1,  < 100,  < 1000 ? is
>> appropriate
>>
>> Can anyone tell me which value is appropriate for lipid membrane, for
>> protein in water, for protein in lipid membrane ?
>>
>>
> There is no absolute rule.  The purpose of EM is just to get the
> simulation system into a configuration that is sufficiently relaxed such
> that dynamics don't implode.  For sensitive free energy calculations and
> normal mode analysis, you need the Fmax to be as low as possible.  For most
> protein systems, Fmax < 1000 is generally reasonable for normal MD, but
> that's just an empirical observation.
>
> -Justin
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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