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vdw parameters for iron
#17283 03/03/08 08:58 AM
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laura Offline OP
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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
laura #17284 03/03/08 11:38 AM
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From parmfile.doc:
Parameters for (G) NONBonded VDW parameters may be specified
in two ways. Initially the Tanford-Kirkwood 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 Tanford-Kirkwood 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 well-depth (epsilon) and the third
term is the (minimum radius)/2. Both formulations use the
Lennard-Jones 6-12 formula to determine the VDW interactions, in the
first method the Tanford-Kirkwood Formula is used to calculate the
well-depth (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 1-4
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
lennart #17285 03/05/08 09:33 PM
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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
jb007 #17286 03/06/08 07:38 AM
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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 well-depth 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
lennart #17287 03/06/08 12:07 PM
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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 non-bonded 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
jb007 #17288 03/06/08 01:03 PM
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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

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