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On 4/28/2011 10:06 AM, Elisabeth wrote:
<blockquote
cite="mid:BANLkTi=yBTi1QPZPNYB+N2mJK-wSAPtNeA@mail.gmail.com"
type="cite">Hi Mark,<br>
<br>
I am excited to see that there is a solution to my issue. I
thought this problem can not be resolved.<br>
<br>
In thermodynamics of polymer solutions, people use some models
(equation of state) in which an interaction parameter K_AB appears
which is defined in terms of interaction energies i.e.
1-K_AB=(E_AB)/(E_AA*E_BB)^0.5.</blockquote>
<br>
Ok - but the important point (as I said before) is how those
energies are defined. Without knowing that, you've no idea what
you're trying to reproduce from the GROMACS numbers.<br>
<br>
<blockquote
cite="mid:BANLkTi=yBTi1QPZPNYB+N2mJK-wSAPtNeA@mail.gmail.com"
type="cite"> One way to obtain this parameter is to manipulate
this K so that equation of state predicts say bubble point data or
density vs. pressure. In this procedure they dont look at
interaction energies E_BB,...and only K is tuned. (or in some
models they deal with E_ij interaction energies and manipulate so
that some properties are fitted to experimental data).<br>
<br>
Now what I am interested in is calculating these interaction
energies by MD and thats why I need to extract pairwise energies
per mol. To double check what I have done with you:<br>
<br>
FOr a system having 4 polymer chains and 100 solvent molecules, I
defined two groups in index file: [polymer] with all atoms of
polymer chains. and [solvent] with all atoms of solvent. and use
energygrps= polymer solvent. Now I have polymer-solvent,
polymer-polymer and solvent-solvent interaction energies (LJ +
Coulomb SR for each pair). <br>
<br>
As you say to normalize this I have to divide by [(4*Np)*(100*Ns)]
where Np and Ns are number of atoms in polymer chain and solvent
molecule. <br>
<br>
1- Did I get your instruction correctly?<br>
</blockquote>
<br>
Yes, that's the sense of my suggestion.<br>
<br>
<blockquote
cite="mid:BANLkTi=yBTi1QPZPNYB+N2mJK-wSAPtNeA@mail.gmail.com"
type="cite">2- The unit of energies is per atom now? I am confused
if its per atom or molecule?<br>
</blockquote>
<br>
The energy of each inter-atom interaction is measured in...
drumroll... kJ/mol. That number is the energy that a mole of such
interactions would have. Adding them up and dividing by the number
of interactions doesn't change anything, except the awkwardness of
articulating what the system now is.<br>
<br>
<blockquote
cite="mid:BANLkTi=yBTi1QPZPNYB+N2mJK-wSAPtNeA@mail.gmail.com"
type="cite">
<br>
3- Since the interaction parameter in the model is defined as 1-
K_AB=(E_AB)/(E_AA*E_BB)^0.5 and the ratio of interaction energies
appear in K, is this normalization sufficient? I mean because of
ratio of energies it seems there is no need to convert these
normalized values to MOL! <br>
</blockquote>
<br>
Maybe. Look up the definitions of those energy quantities. Don't
randomly invent "MOL" as nomenclature... I don't know whether your
emphasis is supposed to differentiate from "mol", nor whether you
intend "mole" or "molecule". Use abbreviations for brevity, but not
so as to impede clarity :-)<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTi=yBTi1QPZPNYB+N2mJK-wSAPtNeA@mail.gmail.com"
type="cite">4- Is it possible to achieve energy per MOL for this
binary system from normalized energies?<br>
<br>
Appreciate your help!<br>
Best :)<br>
<br>
<br>
<br>
<div class="gmail_quote">On 12 April 2011 00:10, Mark Abraham <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">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 text="#000000" bgcolor="#ffffff">
<div>
<blockquote 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>
</div>
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>
<font color="#888888"> <br>
Mark</font>
<div><br>
<br>
<blockquote 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"
target="_blank">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>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>
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