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#793 01/05/04 10:55 AM
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Dear CHARMm users,

I'm running free energy simulations using pert. Could anybody explain me the precise physical meaning of VDWaals and ELEC terms in DYNA results.

Thank you in advance,
Dr. E. Nikitina

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Both terms forms the so-called non-bonded interaction energies and forces.

The vdW term consists of an attractive and a repulsive term (also denoted Lennard-Jones 6-12 interactions) and for two atoms ( i and j ) separated by a distance rij (in Å) and intervened by 3 explicit bonds or more, the additive pair-potential is given by

rm = 0.5*(rim+rjm)
eps = sqrt(epsi*epsj)

EvdW=4*eps[(rm^12)/rij^12) - (rm^6/rij^6)]

and the electrostatic part is Coulombic in nature, thus

Eelec = 332qi*qj/rij

where qi and qj are the charges (in protonunits) on each atom.

and E=Eelec+Evdw

Note that other polyexponentials can be used for the LJ pair-potential, and that rim=sigma^(-5/6) , where sigma is the conventionally termed vdW radii for atom i.

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Note that if you are running with a periodic system, these terms only include primary-primary interactions. The terms beneath them in the output (IMNB and IMEL) contain the corresponding primary-image terms. It is the sum of these terms that is invariant to image centering,..

Also note that if you are using an Ewald method, the electrostatic terms only include the short-range real space term which is the standard electrostatics multiplied by erfc(k*r).

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This is interesting, and I wonder:
What's your opinion about using Ewald-summation techniques in conjuntion with force-fields that has been parameterized under different conditions? - meaning for instance: Would PME unmask eventual ill-defined force-field parameters? Or should one focus even more on refining existing parameters beneficial for less demanding treatment of long-range forces?

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Thank you for your reply. Nevertheless while we run simple molecular dynamics simulation of the small molecule in solution (216 water molecules, PME, MMFF94) the ELEC and VDW terms in output didn’t change significantly, but when we turned on pert procedure (we made two runs: first, we didn’t change any parameters of the system and second we made charge annihilation on the solute molecule) in both cases ELEC and VDW turn to 0.

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rmv Online Content
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Have you tried your calculations using e.g. the TIP3 water model with CHARMM parameters? Perhaps this problem may be related to the use of the MMFF potential. I've had a fair amount of trouble dealing with the "features" of the CHARMM implementation of MMFF.


Rick Venable
computational chemist


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