Yes, that's correct. The sigma-related parameters are given with those
multipliers to feed into a simplified equation (old Fortran codes reducing
math operations).
On Tue, Jul 24, 2018 at 5:02 PM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Sorry about the typo...
>
> sigma_ij = (Rmh[type1] + Rmh[type2])*2^(-1/6)
>
> Matias
>
> ----- Mensaje original -----
> De: "Matias Machado" <mmachado.pasteur.edu.uy>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Martes, 24 de Julio 2018 17:58:15
> Asunto: Re: [AMBER] LJEDIT syntax
>
> Thanks David,
>
> With your comments I was able to implement the special LJ parameters into
> the frcmod file.
>
> However, I notice that the actual parameters read for each atom type are
> "Rm/2" (= Rmh, "Rm half") and "epsilon" (e), same as in the NONBON section.
>
> So sigma_ij = (Rmh[type1] + Rmh[type2])*2^(1/6) and e_ij = sqrt(e[type1] *
> e[type2])
>
> The other important thing is that the section LJEDIT only affects the
> defined interaction (it doesn't overwrite the NONBON section). Indeed these
> three definitions of the A-B interaction render the same prmtop despite
> being different from a conceptual point of view:
>
> LJEDIT
> # type1 type1 Rmh[type1] e[type1] Rmh[type2] e[type2]
> A B 1.5 0.2 1.5 0.2
> A B 3.0 0.2 0.0 0.2
> A B 1.0 0.1 2.0 0.4
>
> By the way, I think this is a very nice feature that introduces a lot of
> flexibility to AMBER (comparable to other popular MD engines), I hope it
> won't be deprecated...
>
> Best,
>
> Matías
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/laboratorios-eng/lsbm]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "David Cerutti" <dscerutti.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Lunes, 23 de Julio 2018 16:09:38
> Asunto: Re: [AMBER] LJEDIT syntax
>
> I'm the culprit here. I came up with that when we thought we needed
> parameters off the usual combining matrix. What the numbers stand for is
> the Lennard-Jones sigma and epsilon of the first atom type when it
> interacts with anything under the normal rules, then the sigma and epsilon
> of the second atom type when it interacts with the first. So all of those
> OW's in the parm14ipq.dat file have the sigma and epsilon of TIP4P-Ew water
> oxygen (the OW parameters are recast from the TIP3P which I sloppily left
> in the list above--TIP4P-Ew is the water model of choice for ff14ipq).
> Then, when type ND interacts with OW, it does so as if the ND has sigma and
> epsilon 2^(5/6) * 1.960000 A and 0.170000 kcal/mol. So the interaction of
> ND and OW takes place according to
>
> sigma = 0.5 * (1.775931 + 1.960000) * 2^(5/6) = 3.3283A
> epsilon = sqrt(0.162750 * 0.170000) = 0.16634 kcal/mol
>
> That's the way LJEDIT works. I'll see about getting this into the manual,
> but it's rare that someone has wanted the feature.
>
> Dave
>
>
>
> On Mon, Jul 23, 2018 at 2:16 PM Matias Machado <mmachado.pasteur.edu.uy>
> wrote:
>
> > Dear AMBER experts,
> >
> > I'm trying to set some Lennard-Jones interactions out-off the combination
> > rule. I was able to do it by using Parmed, however I want to set them in
> a
> > frcmod file so they can be applied by leap without further modification
> of
> > the topology.
> >
> > I know the LJEDIT section (available from amber14 on) would allow me to
> do
> > so, however its syntax is poorly documented, indeed I couldn't find any
> > mention to that keyword in the Amber manuals, nor in the file formats at
> > the AMBER web page [http://ambermd.org/FileFormats.php]
> >
> > The only reference I found was this post in the mailing list [
> > http://dev-archive.ambermd.org/201301/0018.html], in which its
> > implementation is discussed. From those comments, I would expect the
> > following syntax:
> >
> > LJEDIT
> > <Type 1> <Type 2> <R* pair> <Eps pair>
> > ...
> > END
> >
> > However, looking at the implementation of parm14ipq.dat [
> > https://www.ncbi.nlm.nih.gov/pubmed/25328495] and CUFIX
> > (frcmod.ff99cufix) [http://bionano.physics.illinois.edu/CUFIX]
> > I found 4 terms instead of 2 for defining the LJ interaction, my guess is
> > that 1-4 interactions can also be set separately but I'm not sure about
> > that...
> >
> > In any case... what does each set of parameters stand for?
> >
> > Best regards,
> >
> > Matías
> >
> > ------------------------------------
> > PhD.
> > Researcher at Biomolecular Simulations Lab.
> > Institut Pasteur de Montevideo | Uruguay
> > [http://pasteur.uy/en/laboratorios-eng/lsbm]
> > [http://www.sirahff.com]
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Jul 24 2018 - 17:30:03 PDT
