[gmx-users] gmx_saxs sampling frequency

[Evan Lowry]

Yu,

Thanks again. I still do not understand what that will calculate. Do you
have a possible literature reference where I could read about this? If we
modify the values of Coh_b doesn't that invalidate the calculation? Thanks
for your time.

Evan L.

On Mon, Jul 11, 2016 at 2:23 AM, Yu Ogawa <ayogwa at gmail.com> wrote:

> Hi Evan,
> You can find nsfactor.dat in /gromacs/share/top. You can copy it to your
> working directory and modify the values of fourth column (Coh_b) to atomic
> number.
> Hope it could help you.
>
> 2016-07-08 15:39 GMT+02:00 Evan Lowry <evanwlowry at gmail.com>:
>
> > Yu,
> >
> > Thanks for the idea. I see that gmx_sans allows for an optional data file
> > input "nsfactor.dat" but am unsure what that does. Could you provide some
> > details into what exactly goes into the "nsfactor.dat" file and what the
> > output would be? Thanks for your help.
> >
> > Regards,
> >
> > Evan L.
> > On Jul 8, 2016 4:43 AM, "Yu Ogawa" <ayogwa at gmail.com> wrote:
> >
> > > Hi Evan,
> > >
> > > I had the same issue, and could not solve the problem as I did not go
> > into
> > > the source code.
> > > What I did at that time is to use "gmx sans" with modified nsfactor.dat
> > > where I put atomic number instead of scattering length, though I don't
> > know
> > > how appropriate that approach is..
> > >
> > > Yu
> > >
> > > 2016-07-07 16:17 GMT+02:00 Evan Lowry <evanwlowry at gmail.com>:
> > >
> > > > Hello,
> > > >
> > > > I am attempting to use the gmx_saxs tool in order to resolve the
> x-ray
> > > > scattering intensity profile for a trajectory of aggregating
> molecules.
> > > The
> > > > primary peaks (non-log scale) are occurring at q values of about 0.5
> > > 1/nm.
> > > > Unfortunately, the gmx_saxs tool doesn't have a feature to decrease
> the
> > > > grid spacing in q-space. Does anyone know if there is a way to make
> > tool
> > > > calculate with more resolution in the small q range (preferably
> without
> > > > diving into and modifying the module)? Any ideas would be much
> > > appreciated.
> > > >
> > > > Thanks,
> > > >
> > > > Evan L.
> > > > --
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