[gmx-developers] Regarding commit Implementation of WAXS/SAXS refinement in MD!
Anjaiah Nalaparaju
anjai.che at gmail.com
Tue Aug 26 07:21:28 CEST 2014
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
>> --
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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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