[gmx-developers] Gromacs-2016: Win64 quasi-portable

Boris Timofeev boristim at mail.ru
Mon Oct 3 00:50:12 CEST 2016

PS. This is output from file   where the crystal waters not  stripped out  .
With file  where the crystal waters   stripped out the result the same.

Thank you very much.

>Понедельник,  3 октября 2016, 1:01 +03:00 от Justin Lemkul <jalemkul at vt.edu>:
>On 10/2/16 5:42 PM, Boris Timofeev wrote:
>> Good afternoon to all!
>> I did a great job on compilation of the "portable" Gromacs-2016 version on the
>> Win64  platform without cygwin with OpenCL support and  AVX_256/AVX2_256
>> expansions. The project is builded on VS-2015. By small changes in CMakeLists, I
>> managed to achieve that both the "embedded" tests, and regressiontests, are
>> executed after assembly immediately from VS IDE. It was tested on Windows7/
>> Windows10  with IntelCore i3, i5, i7  processors and video cards from Nvidia and
>> AMD. So far it was not succeeded to win  - against the video card from Intel -
>> Intel OpenCL compiler preprocessor is left unfinished, does not recognize
>> directive "-I" and have buggy concatention (##) implementation.
>> It was necessary to realize a primitive preprocessor,  became successful, but
>> all the same calculations (tests and regressiontests) are wrong as it was
>> already metioned here (https://bugs.freedesktop.org/show_bug.cgi?
>> id=94265#add_comment).
>> If it is interesting to community, I am ready to report about some necessary
>> changes in progect and to provide the main CMake-file.
>> There are several questions to developers.
>> 1. The nbnxn_ocl_kernel_nvidia.clh, nbnxn_ocl_kernel_nowarp.clh and
>> nbnxn_ocl_kernel_amd.clh files, if to compare their with kdiff, differ only in
>> comments and lack of unroll pragma for Nvidia. Why not to unite them in one?
>> Where the promised optimization?
>> 2. Why in the Gromacs'a code so many paths to files are embedded up? To start
>> tests without development environment on other computer it is necessary to copy
>> practically all project.
>> 3. A question "on science". When performing an example of
>>  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html ,
>>  pdb2gmx for the aminoacid residue  HIS ("HIZE-branch" on stdout ), unlike all
>> others residue,  gives a nonintegral charge 0.883,  inexplicable with round-off
>> errors.
>> Whether there is no program mistake here?
>I can't speak to points 1 and 2, but here: what is HIZE-branch?  I've never 
>heard of that.  Note, too, that if you're working with a single amino acid with 
>OPLS-AA, you can't rely on the default terminus selection.  You need to choose 
>the zwitterion termini, otherwise the charges will be junk because OPLS-AA makes 
>changes to CA depending on whether the residue is a zwitterion or in a polypeptide.
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>Gromacs Developers mailing list
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