[gmx-developers] Regarding commit Implementation of WAXS/SAXS refinement in MD!
Anjaiah Nalaparaju
anjai.che at gmail.com
Mon Oct 13 11:52:23 CEST 2014
Hello,
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.
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, Björling and Westenhoff, J. Appl.
Cryst. 47 (2014) 1190"
[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."
3. Where the form-factors with displaced volume corrections are calculated
in the code.
Thank you for your time and help.
Best regards
On Tue, Aug 26, 2014 at 1:21 PM, Anjaiah Nalaparaju <anjai.che at gmail.com>
wrote:
> Thank you.
>
> I have noted the new code is completely different from old code. But I am
> still curious to know about the loop used in sfactor.c to compute the
> structure factors.
>
> /*
> * The big loop...
> * compute real and imaginary part of the structure factor for every
> * (kx,ky,kz))
> */
> /*
> * compute the square modulus of the structure factor, averaging on
> the surface
> * kx*kx + ky*ky + kz*kz = krr*krr
> * note that this is correct only for a (on the macroscopic scale)
> * isotropic system.
> */
>
>
> Is there any reference discussing this approach. I want to know the
> rationale behind this implementation.
>
> Thanks again for your time and help.
>
>
>
>
>
> On Mon, Aug 25, 2014 at 7:08 PM, David van der Spoel <spoel at xray.bmc.uu.se
> > wrote:
>
>> On 2014-08-25 11:56, Anjaiah Nalaparaju wrote:
>>
>>> Hello,
>>>
>>> 1. In the previous code to compute structure factors (sfactor.c) there
>>> is a loop
>>> /*
>>> * The big loop...
>>> * compute real and imaginary part of the structure factor for every
>>> * (kx,ky,kz))
>>> */
>>> /*
>>> * compute the square modulus of the structure factor, averaging on
>>> the surface
>>> * kx*kx + ky*ky + kz*kz = krr*krr
>>> * note that this is correct only for a (on the macroscopic scale)
>>> * isotropic system.
>>> */
>>> This loop is no more in the new code "scattering_factors.cpp". May I
>>> know why this loop is used in the previous code. Is this to introduce
>>> orientational averaging?
>>>
>>
>> Note that there is no relation between the previous code and the new one,
>> that is the new code is derived from scratch.
>>
>>
>>
>>> 2. I think sfactor.xml (input file for gmx waxsdebye) is still in the
>>> development stage?
>>>
>> Formally yes, we will implement some tests now to validate it.
>>
>>
>>> Thanks in advance.
>>>
>>>
>>>
>>>
>>> On Fri, Aug 22, 2014 at 4:09 PM, David van der Spoel
>>> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>>>
>>> On 2014-08-22 09:45, Anjaiah Nalaparaju wrote:
>>>
>>> Thank you very much for the response. I did the following.
>>>
>>> 1. git clone git://git.gromacs.org/gromacs.__git
>>> <http://git.gromacs.org/gromacs.git>
>>> <http://git.gromacs.org/__gromacs.git
>>>
>>> <http://git.gromacs.org/gromacs.git>> (to download the master
>>> branch)
>>>
>>>
>>> 2. git fetch https://gerrit.gromacs.org/__gromacs
>>>
>>> <https://gerrit.gromacs.org/gromacs> refs/changes/59/2659/84
>>> && git format-patch -1 --stdout FETCH_HEAD (to apply patch to
>>> the source
>>> code)
>>>
>>> 3. mkdir build and under the build folder $cmake .. -DGMX_MPI=ON
>>> -DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON -DGMX_DEFAULT_SUFFIX=OFF
>>> -DGMX_BINARY_SUFFIX=_mpi -DGMX_LIBS_SUFFIX=_mpi
>>>
>>> 4. Once the installation completed, under the bin folder I see
>>> all the
>>> tools same as before and didn't see any new tool related to
>>> waxsdebye.
>>> Version shows VERSION 5.1-dev-20140821-d9c0e41.
>>>
>>> May I know what is the name of new tool for WAXS/SAXS
>>> calculation.
>>>
>>> gmx help commands
>>> should show the command to be
>>> gmx waxsdebye
>>>
>>> Thanks in advance.
>>>
>>>
>>>
>>> On Fri, Aug 22, 2014 at 1:51 PM, David van der Spoel
>>> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>>> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>>
>>> wrote:
>>>
>>> On 2014-08-22 05:38, Anjaiah Nalaparaju wrote:
>>>
>>> Dear Dr. David van der Spoel,
>>>
>>> I am interested in the module you have been developing
>>> for
>>> WAXS/SAXS. I
>>> was introduced to this patch by Dr.Alexey Shvestov. I
>>> have two
>>> queries
>>> related to the this module and I have been suggested to
>>> contact
>>> you to
>>> get the accurate information on my queries.
>>>
>>> 1. I have downloaded the latest code (patch 83), if I
>>> install
>>> this copy
>>> I still didn't get the gmx waxsdebye or g_waxdebye tool
>>> to use
>>> under bin
>>> folder. Could you please guide me how can we try and
>>> test this
>>> tool now.
>>>
>>> You download the latest master branch, then apply the patch
>>> to the
>>> source code, by copying the link on the gerrit web site and
>>> rebuild
>>> and install. This works for us. We are still doing a bit of
>>> development but it is almost finished.
>>>
>>>
>>>
>>> 2. I am just curious to know why the same approach as
>>> g_sans has not
>>> been used in this module. I mean working in the real
>>> space was
>>> not chosen.
>>>
>>> In fact I don't know, Alexey has suggested the approaches
>>> are
>>> similar but I have not looked into it I must admit.
>>>
>>>
>>> Thanks in advance for your time and help. Sorry for
>>> sending mail
>>> to your
>>> personal email id.I have posted part of my queries in
>>> gmxdevelopers list
>>> but didnt get response.
>>>
>>> Sorry about that, but let's move the discussion back to the
>>> developers list so that others can join in as well. Please
>>> post
>>> further questions there in other words.
>>>
>>>
>>> Best regards,
>>> Anjaiah
>>>
>>>
>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205
>>> <tel:%2B46184714205>
>>> <tel:%2B46184714205>.
>>> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>>> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
>>>
>>> http://folding.bmc.uu.se
>>>
>>>
>>>
>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205
>>> <tel:%2B46184714205>.
>>> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>>> http://folding.bmc.uu.se
>>> --
>>> Gromacs Developers mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/__Support/Mailing_Lists/GMX-__developers_List
>>> <http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List>
>>> before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>>>
>>> <http://www.gromacs.org/Support/Mailing_Lists>
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/__mailman/listinfo/gromacs.org__
>>> _gmx-developers
>>> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
>>> gmx-developers>
>>> or send a mail to gmx-developers-request at __gromacs.org
>>> <mailto:gmx-developers-request at gromacs.org>.
>>>
>>>
>>>
>>>
>>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>> --
>> 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.
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20141013/daf8581c/attachment-0001.html>
More information about the gromacs.org_gmx-developers
mailing list