<HTML><BODY>PS. This is output from file <span style="font-family: Arial; font-size: medium;" data-mce-style="font-family: Arial; font-size: medium;"> where the crystal waters not <span style="font-family: Arial; font-size: medium;" data-mce-style="font-family: Arial; font-size: medium;">stripped out </span>.<br></span>With file <span style="font-family: Arial; font-size: medium;" data-mce-style="font-family: Arial; font-size: medium;">where the crystal waters</span> <span style="font-family: Arial; font-size: medium;" data-mce-style="font-family: Arial; font-size: medium;">stripped out the result the same.<br><br></span>Thank you very much.<br><br><br><blockquote style="border-left:1px solid #0857A6; margin:10px; padding:0 0 0 10px;">
Понедельник, 3 октября 2016, 1:01 +03:00 от Justin Lemkul <jalemkul@vt.edu>:<br>
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On 10/2/16 5:42 PM, Boris Timofeev wrote:<br>
><br>
> Good afternoon to all!<br>
><br>
> I did a great job on compilation of the "portable" Gromacs-2016 version on the<br>
> Win64 platform without cygwin with OpenCL support and AVX_256/AVX2_256<br>
> expansions. The project is builded on VS-2015. By small changes in CMakeLists, I<br>
> managed to achieve that both the "embedded" tests, and regressiontests, are<br>
> executed after assembly immediately from VS IDE. It was tested on Windows7/<br>
> Windows10 with IntelCore i3, i5, i7 processors and video cards from Nvidia and<br>
> AMD. So far it was not succeeded to win - against the video card from Intel -<br>
> Intel OpenCL compiler preprocessor is left unfinished, does not recognize<br>
> directive "-I" and have buggy concatention (##) implementation.<br>
> It was necessary to realize a primitive preprocessor, became successful, but<br>
> all the same calculations (tests and regressiontests) are wrong as it was<br>
> already metioned here (https://bugs.freedesktop.org/show_bug.cgi?<br>
> id=94265#add_comment).<br>
><br>
> If it is interesting to community, I am ready to report about some necessary<br>
> changes in progect and to provide the main CMake-file.<br>
><br>
> There are several questions to developers.<br>
><br>
> 1. The nbnxn_ocl_kernel_nvidia.clh, nbnxn_ocl_kernel_nowarp.clh and<br>
> nbnxn_ocl_kernel_amd.clh files, if to compare their with kdiff, differ only in<br>
> comments and lack of unroll pragma for Nvidia. Why not to unite them in one?<br>
> Where the promised optimization?<br>
><br>
> 2. Why in the Gromacs'a code so many paths to files are embedded up? To start<br>
> tests without development environment on other computer it is necessary to copy<br>
> practically all project.<br>
><br>
> 3. A question "on science". When performing an example of<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html</a>,<br>
> pdb2gmx for the aminoacid residue HIS ("HIZE-branch" on stdout ), unlike all<br>
> others residue, gives a nonintegral charge 0.883, inexplicable with round-off<br>
> errors.<br>
> Whether there is no program mistake here?<br>
><br>
<br>
I can't speak to points 1 and 2, but here: what is HIZE-branch? I've never <br>
heard of that. Note, too, that if you're working with a single amino acid with <br>
OPLS-AA, you can't rely on the default terminus selection. You need to choose <br>
the zwitterion termini, otherwise the charges will be junk because OPLS-AA makes <br>
changes to CA depending on whether the residue is a zwitterion or in a polypeptide.<br>
<br>
-Justin<br>
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-- <br>
==================================================<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Ruth L. Kirschstein NRSA Postdoctoral Fellow<br>
<br>
Department of Pharmaceutical Sciences<br>
School of Pharmacy<br>
Health Sciences Facility II, Room 629<br>
University of Maryland, Baltimore<br>
20 Penn St.<br>
Baltimore, MD 21201<br>
<br>
<a href="mailto:jalemkul@outerbanks.umaryland.edu">jalemkul@outerbanks.umaryland.edu</a> | (410) 706-7441<br>
<a href="http://mackerell.umaryland.edu/~jalemkul" target="_blank">http://mackerell.umaryland.edu/~jalemkul</a><br>
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