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

[David van der Spoel]

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