[gmx-users] energy comparison

Edward Deira edward.deira at gmail.com
Tue Oct 2 20:45:32 CEST 2012

not that off-base, actually. one of my aims is to compare two different
proteins with the same ligand and try to figure out which system is
energetically more favourable without having to go through qm/mm. so i
suppose the proper way would be estimating the "absolute" free energy of
the system.

can i do that with gromacs ? i know that computing deltaG is ***trivial***
(not the best word,i know), but what about "absolute" values?
On Oct 2, 2012 7:26 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

> On 10/2/12 12:49 PM, Edward Deira wrote:
>> Dear all,
>>  From the computational side of the question, can one compare the final
>> energy values at the end of a simulation ? Are those energy values are
>> meaningful ?
>> Can I, with proper chemical judgement, say that a lower (more negative)
>> value will correspond to a more "stable" system ?
> I will make several assumptions about what you're dealing with to try to
> answer this question.  If I'm off-base, then please be (much) more specific
> about what you're doing.  For a "normal" case of some solute in water, the
> potential energy is dominated by the water itself.  The value of energy
> from a single snapshot really doesn't mean much, and the only comparison
> you might be able to make would be between identical systems, i.e.
> replicate simulations of the same starting configuration.  If the systems
> differ at all in their contents, you're comparing apples and oranges since
> the potential energy is an extensive property.
> There are considerably more robust approaches to real free energy analysis
> coupled with conformational sampling that one can do.  I would not be
> inclined to believe a stability argument based on a statement like "the
> potential energy of snapshot A was lower than that of snapshot B, so
> therefore configuration A is more stable."
> -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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