[gmx-users] Energy minimization
Kieu Thu Nguyen
kieuthu2212 at gmail.com
Sat Feb 23 13:35:30 CET 2013
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
>> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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