[gmx-developers] Regarding commit Implementation of WAXS/SAXS refinement in MD!
Alexander Björling
alex.bjorling at gmail.com
Tue Oct 14 10:13:45 CEST 2014
> Date: Mon, 13 Oct 2014 22:03:50 +0800
> From: Anjaiah Nalaparaju <anjai.che at gmail.com>
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] Regarding commit Implementation of
> WAXS/SAXS refinement in MD!
> Message-ID:
> <CANEpNGj+Rdy9o+zV7e-vmBMoM11u8go1iR9Y-xH_WzpYT=
> TNSQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Thank you for providing a detailed explanation.
>
> Actually I should focus only on asking about all atom form factors table
> which is " sfactor_atom_nods_Fourier.xml ". In this there is no solvent
> displaced correction so we no need to use any polynomial correction. I
> suppose the coefficients in these table should be close to the cromer-mann
> coefficients (from quantum calculations) or to be in a form to use in the
> following equation to calculate atomic form factor.
> [image: Inline image 1]
>
> As I can see the coefficients given in the .xml file are very different I
> would like to know what is the equation used to calculate atomic form
> factor. In principle, whatever the method or coefficients we use the atomic
> factor at q=0 will be equal to atom number. I am not clear how this is
> satisfied from your coefficients given in " sfactor_atom_nods_Fourier.xml
> ". For example for atom "Carbon" I expect sum of a1 to a5 should be equal
> to 6.
> Please correct me if I have mistaken any concept in your implementation.
>
Again, the numbers in the xml files are _not_ Cromer-Mann parameters. The
numeric scattering factors are calculated for the appropriate q-grid in
scattering_factors.cpp.
>
> Thanks for your time and kind help.
> Best regards
>
>
>
>
> On Mon, Oct 13, 2014 at 6:26 PM, Alexander Bj?rling <
> alex.bjorling at gmail.com
> > wrote:
>
> >
> > From: Anjaiah Nalaparaju <anjai.che at gmail.com>
> >>
> >> My question is related to the unmerged patch for module waxsdebye.
> >>
> >> 1. Can anybody tell the reference for the form factor
> >> coefficients(a1-a5,b1-b5,p1-p3) in file "sfactor_atom_nods_Fourier.xml"
> or
> >> all the new .xml files on sfactors. These number look very much
> different
> >> from the sfactor.dat which are cromer-mann coefficients.
> >>
> > There is no reference (yet). The numbers are different because it's a
> > different parametrization. Since solvent-corrected form factors have a
> more
> > complex shape, we've used a short Fourier sum plus a polynomial, instead
> of
> > gaussians. The form factor is calculated from these parameters in
> > src/gromacs/waxsdebye/scattering_factors.cpp.
> >
> >
> >>
> >> 2. If we use the following equation to calculate atomic form factors, at
> >> q=0 sum of co-eff a1 to a5 should be equal to the form factor value at
> >> q=0
> >> given in the publication "Niebling, Bj?rling and Westenhoff, J. Appl.
> >> Cryst. 47 (2014) 1190"
> >>
> > No they shouldn't, there's also a polynomial there. Again, see
> > scattering_factors.cpp. Have that code print out the scattering factors
> if
> > you would like to test them.
> >
> >
> >> [image: View the MathML source]
> >>
> >> But seems the coefficients in .xml files are not corresponding to this
> >> equation.
> >>
> >> 3. How can the coefficients after displaced volume correction can be a
> >> constant value ( sfactor_atom_ds_Fourier.xml), as the displaced volume
> >> correction term also function of "q". "Svergun, Barberato and Koch, J
> >> Appl.
> >> Cryst. 27 (1995) 768."
> >>
> > I'm not sure what you mean by "constant value".
> >
> >
> >>
> >> 3. Where the form-factors with displaced volume corrections are
> >> calculated
> >> in the code.
> >>
> > The displaced volume corrections are not done in the code. The scattering
> > factors with or without the correction (depending on which xml file is
> > used) are calculated in scattering_factors.cpp.
> >
> >
> > --
> > Gromacs Developers mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
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> > or send a mail to gmx-developers-request at gromacs.org.
> >
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> ------------------------------
>
> Message: 2
> Date: Tue, 14 Oct 2014 12:38:22 +0800
> From: Anjaiah Nalaparaju <anjai.che at gmail.com>
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] Regarding commit Implementation of
> WAXS/SAXS refinement in MD!
> Message-ID:
> <
> CANEpNGiqX9wCH4zDuVQduWUSVJh9ed4rShadgd_XUOHQW39fWQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> I understood the coefficients in .xml file. There is a coefficient "a0",
> this is taking care of formfactor value at q=0.
>
> Best regards
>
> On Mon, Oct 13, 2014 at 10:03 PM, Anjaiah Nalaparaju <anjai.che at gmail.com>
> wrote:
>
> > Thank you for providing a detailed explanation.
> >
> > Actually I should focus only on asking about all atom form factors table
> > which is " sfactor_atom_nods_Fourier.xml ". In this there is no solvent
> > displaced correction so we no need to use any polynomial correction. I
> > suppose the coefficients in these table should be close to the
> cromer-mann
> > coefficients (from quantum calculations) or to be in a form to use in the
> > following equation to calculate atomic form factor.
> > [image: Inline image 1]
> >
> > As I can see the coefficients given in the .xml file are very different I
> > would like to know what is the equation used to calculate atomic form
> > factor. In principle, whatever the method or coefficients we use the
> atomic
> > factor at q=0 will be equal to atom number. I am not clear how this is
> > satisfied from your coefficients given in " sfactor_atom_nods_Fourier.xml
> > ". For example for atom "Carbon" I expect sum of a1 to a5 should be equal
> > to 6.
> >
> > Please correct me if I have mistaken any concept in your implementation.
> >
> > Thanks for your time and kind help.
> > Best regards
> >
> >
> >
> >
> > On Mon, Oct 13, 2014 at 6:26 PM, Alexander Bj?rling <
> > alex.bjorling at gmail.com> wrote:
> >
> >>
> >> From: Anjaiah Nalaparaju <anjai.che at gmail.com>
> >>>
> >>> My question is related to the unmerged patch for module waxsdebye.
> >>>
> >>> 1. Can anybody tell the reference for the form factor
> >>> coefficients(a1-a5,b1-b5,p1-p3) in file "sfactor_atom_nods_Fourier.xml"
> >>> or
> >>> all the new .xml files on sfactors. These number look very much
> different
> >>> from the sfactor.dat which are cromer-mann coefficients.
> >>>
> >> There is no reference (yet). The numbers are different because it's a
> >> different parametrization. Since solvent-corrected form factors have a
> more
> >> complex shape, we've used a short Fourier sum plus a polynomial,
> instead of
> >> gaussians. The form factor is calculated from these parameters in
> >> src/gromacs/waxsdebye/scattering_factors.cpp.
> >>
> >>
> >>>
> >>> 2. If we use the following equation to calculate atomic form factors,
> at
> >>> q=0 sum of co-eff a1 to a5 should be equal to the form factor value at
> >>> q=0
> >>> given in the publication "Niebling, Bj?rling and Westenhoff, J. Appl.
> >>> Cryst. 47 (2014) 1190"
> >>>
> >> No they shouldn't, there's also a polynomial there. Again, see
> >> scattering_factors.cpp. Have that code print out the scattering factors
> if
> >> you would like to test them.
> >>
> >>
> >>> [image: View the MathML source]
> >>>
> >>> But seems the coefficients in .xml files are not corresponding to this
> >>> equation.
> >>>
> >>> 3. How can the coefficients after displaced volume correction can be a
> >>> constant value ( sfactor_atom_ds_Fourier.xml), as the displaced volume
> >>> correction term also function of "q". "Svergun, Barberato and Koch, J
> >>> Appl.
> >>> Cryst. 27 (1995) 768."
> >>>
> >> I'm not sure what you mean by "constant value".
> >>
> >>
> >>>
> >>> 3. Where the form-factors with displaced volume corrections are
> >>> calculated
> >>> in the code.
> >>>
> >> The displaced volume corrections are not done in the code. The
> scattering
> >> factors with or without the correction (depending on which xml file is
> >> used) are calculated in scattering_factors.cpp.
> >>
> >>
> >> --
> >> Gromacs Developers mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> >> or send a mail to gmx-developers-request at gromacs.org.
> >>
> >
> >
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>
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