[gmx-users] multicomponent system- units
Mark.Abraham at anu.edu.au
Thu Apr 28 04:01:53 CEST 2011
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.
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
> 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
> 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 :-)
> 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.Abraham at anu.edu.au
> <mailto:Mark.Abraham at 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.
>> 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..
>> On 9 April 2011 20:56, Mark Abraham <Mark.Abraham at anu.edu.au
>> <mailto:Mark.Abraham at 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...
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