[gmx-developers] Regarding commit Implementation of WAXS/SAXS refinement in MD!
David van der Spoel
spoel at xray.bmc.uu.se
Mon Aug 25 13:08:36 CEST 2014
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
> --
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--
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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