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

Anjaiah Nalaparaju anjai.che at gmail.com
Fri Aug 22 09:45:05 CEST 2014

Thank you very much for the response. I did the following.

1. git clone git://git.gromacs.org/gromacs.git (to download the master

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

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.

Thanks in advance.

On Fri, Aug 22, 2014 at 1:51 PM, David van der Spoel <spoel at xray.bmc.uu.se>

> 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.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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