vdw parameters for iron

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Dear all, could anybody explain me the vdw parameters for Fe? (i.e. epsilon=0?, what is the first "ignored" column and why it is zero for the other atom types but not for Fe? ...)
Thank you very much for your help. Laura
!atom ignored epsilon Rmin/2 ignored ... FE 0.010000 0.000000 0.650000 ! ALLOW HEM



Re: vdw parameters for iron

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From parmfile.doc: Parameters for (G) NONBonded VDW parameters may be specified in two ways. Initially the TanfordKirkwood Formula was used where the atom polarizabilities, Number of effective electrons, and (minimum radius)/2 were required. In this formulation the first term following the atom type is the atom polarizability, the second term is the number of effective electrons and must be positive in order to specify the TanfordKirkwood Formula and the third term is the (minimum radius)/2. If the second term is negative, then the first number is ignored, the second term is the welldepth (epsilon) and the third term is the (minimum radius)/2. Both formulations use the LennardJones 612 formula to determine the VDW interactions, in the first method the TanfordKirkwood Formula is used to calculate the welldepth (epsilon) and in the second method it is used directly. With both formulations a second set of 3 numbers may be specified to indicate the VDW parameters to be used for the calculation of 14 nonbonded interactions. Wildcards (*, %, etc. see MISCOM.DOC) may be used with the NONBond as well as the NBFIX and HBOND sections of the parameter file.
Lennart Nilsson Karolinska Institutet Stockholm, Sweden



Re: vdw parameters for iron

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The problem with the listing of rmin as rmin/2 is that it will impair the value of eps  that is  the potential well depth will not scale with a factor 2 (but rather the sqrt (eps1*eps2)) because of the combination rules used. Then the "tuning" of each individual eps will look different if one takes into account the actual radii of the atoms and compute the solvation free energy via the Poisson eq.



Re: vdw parameters for iron

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Hej Johan, I'm not quite sure I understand what you are worried about. Using Rmin or Rmin/2 (or sigma) in the parameter file are of course completely equivalent choices (and CHARMM happens to expect Rmin/2), and they do not influence the welldepth at all. The combination rule for eps is sqrt(eps1*eps2) as you say, but that has nothing to do with Rmin.
Lennart Nilsson Karolinska Institutet Stockholm, Sweden



Re: vdw parameters for iron

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Hi, What I meant is that if one would use the whole Rmin (instead of the tabulated Rmin/2) in fitting the eps1 and eps2 for two atoms not explicitly bonded, then the epsilon would look different depending on whether the radii is Rmin/2 or just Rmin. Basically, the eps is larger for the Rmin/2 values, but have to be smaller if the whole Rmin is used instead for reproducing the same interatomic distances (as for the Rmin/2) in the nonbonded atom pair. It's probably fine as is, but may lead to undesired surprises in cases where the atom parameters are invented, duplicated, imported or transferred from other sources than the CHARMM force field itself. There are at least a few cases in the force field, where the Rmin/2 actually looks like the Rmin to me. At least w/r to radii in the periodic system or for a radii giving the 'correct' electrostatic free energy of solvation, Gelec, from the Poisson (Boltzmann) equation. Now, if these examples would have their radii multiplied by 2, then the Gelec would look different.
So to me it seem's there are some atomic parameters that need revision in the CHARMM force field.



Re: vdw parameters for iron

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But CHARMM uses Rmin when computing the LJ potential. There is a difference between what is in the parameter table and how it is actually used in the calculation. The combination rule is Rmin(i,j) = Rmin(i)/2 + Rmin(j)/2, and since CHARMM expects Rmin/2 to be in the table it does not divide this value by two again.
Lennart Nilsson Karolinska Institutet Stockholm, Sweden




