On 4/28/2011 10:06 AM, Elisabeth wrote:
Hi Mark,
I am excited to see that there is a solution to my issue. I thought
this problem can not be resolved.
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.
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.
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).
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:
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).
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.
1- Did I get your instruction correctly?
Yes, that's the sense of my suggestion.
2- The unit of energies is per atom now? I am confused if its per atom
or molecule?
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.
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!
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 :-)
Mark
4- Is it possible to achieve energy per MOL for this binary system
from normalized energies?
Appreciate your help!
Best :)
On 12 April 2011 00:10, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
Hello Mark,
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.
So how did they compute these interaction energies?
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.
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.
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.
Mark
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?
Please guide me, I am stuck on this..
Thanks,
On 9 April 2011 20:56, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 8/04/2011 12:18 PM, Elisabeth wrote:
Hello everyone,
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.
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.
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...
Mark
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