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From: David Cerutti <dscerutti.gmail.com>

Date: Tue, 24 Jul 2018 20:05:22 -0400

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
*

*> >
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

*> _______________________________________________
*

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*

*> AMBER.ambermd.org
*

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*

*>
*

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Received on Tue Jul 24 2018 - 17:30:03 PDT

Date: Tue, 24 Jul 2018 20:05:22 -0400

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:

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Received on Tue Jul 24 2018 - 17:30:03 PDT

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