[gmx-developers] Regarding commit Implementation of WAXS/SAXS refinement in MD!

[Anjaiah Nalaparaju]

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?

2. I think sfactor.xml (input file for gmx waxsdebye) is still in the
development stage?

Thanks in advance.




On Fri, Aug 22, 2014 at 4:09 PM, David van der Spoel <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> (to download the master branch)
>>
>>
>> 2. git fetch 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>> 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>.
>>     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.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
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