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. 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? 2- The unit of energies is per atom now? I am confused if its per atom or molecule? 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! 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> 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> 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 >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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