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Total and dihedral energies ffrom MD simulations

  1. Oct 8, 2008 #1
    Hi guys,
    I hope you can give me any idea about:

    After a long molecular dynamic simulation of a polymer under periodic boundary conditions, dihedral and total energies are lower than zero, (negative). do you know the physical meaning of that result?

    thanks for reading and for your help

    jspock
     
  2. jcsd
  3. Oct 9, 2008 #2

    Redbelly98

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    Welcome to PF.

    Since nobody else has responded yet, I'll go ahead and hazard a simple guess--though I have very little experience with MD simulations myself.

    Is it as simple as the total kinetic energy is not enough to overcome the (negative) potential energy of the various bonds and/or attractions among the particles?

    Sorry if you've thought of that and ruled it out, as I have no idea of your background or experience.
     
  4. Oct 13, 2008 #3
    Thanks Redbelly, you are right but after your comments and some more reading I found out a best answer:

    energy on MD simulations, depends very much on which force field you use, and the particular form they use for the dihedral term; many use periodic terms, including several terms for one dihedral; i.e.

    U = K*(1 + n*cos(PHI - PHIeq))

    so depending on, it is possible to easily get negative dihedral energies.

    Total energies are usually negative, because it means that the system is favorable (the lower the better).


    thanks

    javier
     
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