<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, May 29, 2014 at 8:10 AM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div class=""><p dir="ltr"><br>
On May 29, 2014 12:55 AM, "Jorge de Antonio" <<a href="mailto:j.de.antonio@grs-sim.de" target="_blank">j.de.antonio@grs-sim.de</a>> wrote:<br>
><br>
> Hi,<br>
><br>
> Thanks again for your help. Also I see that the structure in the gromacs 4.5 and 5.0 has changed. I had some extra c files in the kernel directory in src in the old version. Those functions defined were called in the md.c. Now I came up with the question… where should I put these extra files in (5.0 version)? My first attempt was to paste them (with the corresponding changes) into src/programs/mdrun/.</p>
</div><p dir="ltr">Yes, that should work fine.</p><div class="">
<p dir="ltr">> I would appreciate if someone can help about how the files and directories are set in the source code. I haven’t found anything in the documentation.</p>
</div><p dir="ltr">It's hard to say, because 90 percent of it depends on 90 percent of it, and all changing. Stuff will continue to move around while we continue to re-create some modularity. src/programs/mdrun, src/gromacs/{gmxlib,mdlib,gmxana,gmxpreprocess,legacyheaders} are all buckets of semi-random stuff historically located in similarly named directories. Many of those locations will disappear eventually. Other directories have some more modularity, but the quality of that expression will vary a lot. There is Doxygen available for much of the newly written code, which describes some of the organisation, but I have not yet written the code to deploy it automatically to the web.</p>
</blockquote><div><br></div><div>Though there is <a href="http://jenkins.gromacs.org/job/Doxygen_Gerrit_5_0/javadoc/">http://jenkins.gromacs.org/job/Doxygen_Gerrit_5_0/javadoc/</a> as a temporary measure.</div><div><br></div>
<div>Mark </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><span class=""><font color="#888888">
<p dir="ltr">Mark</p></font></span><div class=""><div class="h5">
<p dir="ltr">> Thanks again for your time.<br>
> Best,<br>
><br>
> Jorge<br>
><br>
><br>
> On 22 May 2014, at 15:18, Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>> wrote:<br>
><br>
>> Hi,<br>
>><br>
>> Clues for this might be found by examining the git history for that file. Get the GROMACS git repository and use something like<br>
>><br>
>> git log -- src/gromacs/gmxana/gmx_chi.c src/tools/gmx_chi.c<br>
>><br>
>> to see the history for whatever that file was called at the time. This should give you some metadata about the change.<br>
>><br>
>> Mark<br>
>><br>
>> On May 21, 2014 12:40 PM, "Jorge de Antonio" <<a href="mailto:j.de.antonio@grs-sim.de" target="_blank">j.de.antonio@grs-sim.de</a>> wrote:<br>
>>><br>
>>> Dear developers,<br>
>>><br>
>>> I’ve noticed that there is a substancial change in the gmx_chi.c file (located in /src/gromacs/gmxana) when comparing to the 4.5.1. The thing is I must modify the variable int naa (in the histogramming function) but that variable doesn’t exist anymore in the new version. I guess is somehow related with the gmx_residue_type_t rt. I would appreciate some help in getting a better understanding of this function. Thanks a lot.<br>
>>><br>
>>> Cheers,<br>
>>> Jorge<br>
>>> --<br>
>>> Gromacs Developers mailing list<br>
>>><br>
>>> * Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br>
>>><br>
>>> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
>>><br>
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>><br>
>> -- <br>
>> Gromacs Developers mailing list<br>
>><br>
>> * Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br>
>><br>
>> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
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>> <a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br>
><br>
><br>
> X-Antivirus: avast! (VPS 14052700) X-Antivirus-Status: Clean Subject: Re: [gmx-developers] About gmx_chi.c in 5.0 Content-Type: text/html; charset="windows-1252" X-Apple-Auto-Saved: 1 X-Universally-Unique-Identifier: 4A2BE900-3FFA-4320-B2CC-35F35B108D0D X-Apple-Mail-Remote-Attachments: YES From: Jorge de Antonio X-Apple-Base-Url: x-msg://2/ In-Reply-To: X-Apple-Windows-Friendly: 1 Date: Wed, 28 May 2014 18:24:50 +0200 X-Apple-Mail-Signature: Content-Transfer-Encoding: quoted-printable Message-ID: <<a href="mailto:69FD7C6B-459D-42DE-AE55-6F2542756B98@rwth-aachen.de" target="_blank">69FD7C6B-459D-42DE-AE55-6F2542756B98@rwth-aachen.de</a>> References: X-Uniform-Type-Identifier: com.apple.mail-draft To: MIME-Version: 1.0<br>
> Thanks again. Also I see that the structure in the gromacs 4.5 and 5.<br>
><br>
><br>
> On 22 May 2014, at 15:18, Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>> wrote:<br>
><br>
>> Hi,<br>
>><br>
>> Clues for this might be found by examining the git history for that file. Get the GROMACS git repository and use something like<br>
>><br>
>> git log -- src/gromacs/gmxana/gmx_chi.c src/tools/gmx_chi.c<br>
>><br>
>> to see the history for whatever that file was called at the time. This should give you some metadata about the change.<br>
>><br>
>> Mark<br>
>><br>
>> On May 21, 2014 12:40 PM, "Jorge de Antonio" <<a href="mailto:j.de.antonio@grs-sim.de" target="_blank">j.de.antonio@grs-sim.de</a>> wrote:<br>
>>><br>
>>> Dear developers,<br>
>>><br>
>>> I’ve noticed that there is a substancial change in the gmx_chi.c file (located in /src/gromacs/gmxana) when comparing to the 4.5.1. The thing is I must modify the variable int naa (in the histogramming function) but that variable doesn’t exist anymore in the new version. I guess is somehow related with the gmx_residue_type_t rt. I would appreciate some help in getting a better understanding of this function. Thanks a lot.<br>
>>><br>
>>> Cheers,<br>
>>> Jorge<br>
>>> --<br>
>>> Gromacs Developers mailing list<br>
>>><br>
>>> * Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br>
>>><br>
>>> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
>>><br>
>>> * For (un)subscribe requests visit<br>
>>> <a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br>
>><br>
>> -- <br>
>> Gromacs Developers mailing list<br>
>><br>
>> * Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br>
>><br>
>> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
>><br>
>> * For (un)subscribe requests visit<br>
>> <a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br>
><br>
><br>
><br>
> --<br>
> Gromacs Developers mailing list<br>
><br>
> * Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br>
><br>
> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
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</p>
</div></div></blockquote></div><br></div></div>