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<blockquote
cite="mid:BANLkTimS+0UVTMC3rD+tffVGJr4hL0GaKA@mail.gmail.com"
type="cite">Hello Mark,<br>
<br>
Thank you for your reply. I have already created the energy
groups. I am trying to validate pairwise energy values (nonbonded)
with some other work ( a thermodynamic model) where they fit these
AA AB BB (E_AA, E_AB, E_BB) energies so that some phase diagrams
are reproduced. The pairwise energies defined in the model are in
KJ/mol. <br>
</blockquote>
<br>
So how did they compute these interaction energies?<br>
<br>
The energy quantity GROMACS reports for a microstate can be best
thought of as the energy one would have for a mole of such
microstates. Alternatively, divide by N_A and that's the energy for
this microstate - but that's a much less convenient number to use.<br>
<br>
To obtain a quantity that is independent of the number of particles,
you have to normalize for the number of interactions of each type.
If these are all pairwise between atoms in a unary system, then you
need to divide by the square of the number of atoms. So for the
mixed interaction energy of the binary system, you divide by the
product of the respective numbers of atoms.<br>
<br>
You should also verify that these actually are converged observables
that are independent of the number of particles by simulating
replicates from different starting configurations, and systems of
different sizes.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTimS+0UVTMC3rD+tffVGJr4hL0GaKA@mail.gmail.com"
type="cite">
Since my energies are not per mol, my results are useless,
unfortunately. As they depend on number of molecules in the
system. To achieve my goal, what do you suggest? For a binary
system, can I run two separate simulations for pure A and B in
which case using -nmol gives per mol energies and somehow predict
AB from them? Does this make sense?<br>
<br>
Please guide me, I am stuck on this..<br>
<br>
Thanks,<br>
<br>
<div class="gmail_quote">On 9 April 2011 20:56, Mark Abraham <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>
<div></div>
<div class="h5">On 8/04/2011 12:18 PM, Elisabeth wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hello everyone,<br>
<br>
I have encountered a simple problem. For a homogenous
system what g_energy reports is dependent on the system
size and one needs to use -nmol option to divide
energies by number of molecules to obtain per mol
values.<br>
<br>
I am attempting to extract interaction energies between
species in a three component system. I am puzzled how
this can be achieved for such a system. Say there are
100 solvent, 20 solute A and 10 B molecules.<br>
</blockquote>
<br>
</div>
</div>
You would have to start by defining energy groups that contain
relevant sets of molecules (see manual). Even once you've got
them, the group-wise energies won't mean much of anything.
Every observable is dependent on the configuration microstate,
and unless you can estimate the relative population of
different microstates to estimate a free energy...<br>
<br>
Mark<br>
<font color="#888888">
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</blockquote>
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