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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>In the Makefiles in kernel, tools and ngmx you will see that all binaries<br>depend on gmxlib and mdlib.<br>So if you type make in the top level directory or in src/kernel,<br>first bondfree.c will be compiled and put into the gmxlib library,<br>in kernel make will then notice that gmxlib is new and relink everything.<br><br>If you only type make (mdrun) in kernel, you new potential will not be in there.<br>Typing make in src or the top level dir is always safe.<br><br>Berk<br></div><br><br><hr id="stopSpelling">> Date: Wed, 22 Oct 2008 10:06:44 -0400<br>> From: jianzou@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Re: modify bondfree.c and recompile<br>> <br>> Hi Mark, David and Bess,<br>> <br>> Thank you all for the suggestions.<br>> <br>> <br>> I know the dependency has to be somewhere in the Makefiles or the<br>> files they include but I cannot find it. What I am doing is simply<br>> "make" under top-level source directory followed by make install. In<br>> this case, the content of all the files (except the RC files) under<br>> bin and lib will be rebuild and differ from the previous build, even<br>> from the same source.<br>> <br>> Berk told me to do "make" in src/gmxlib. I checked the top-level<br>> Makefile and the the rules for "make mdrun" is "make" under<br>> src/gmxlib, src/mdlib and src/kernel, so it seems for my case "make<br>> mdrun" then "make install-mdrun" should be enough to update the<br>> binary, but how about the library?<br>> <br>> The potential I am working is 1D only instead of 3D, therefore the<br>> tabulated bonded/nonbond potential may not apply to my problem.<br>> "Walls" with wall_type=table in gmx4 could be a solution. But I do<br>> not find the implementation details like Chapter 6.7 for tabulated<br>> nonbond interaction, and therefore do not know how to make<br>> interactions of each atomtype with the wall different.<br>> <br>> <br>> Hi Yang He,<br>> <br>> I started from Appendix B.4, where the files to be modified for bonded<br>> potential are listed (Files No.6 and No.12 are the same). You may also<br>> have a look at include/physics.h and include/vec.h.<br>> <br>> <br>> Regards,<br>> <br>> Jian<br>> <br>> On Wed, Oct 22, 2008 at 3:40 AM, <gmx-users-request@gromacs.org> wrote:<br>> ><br>> > Message: 1<br>> > Date: Wed, 22 Oct 2008 11:57:46 +1100<br>> > From: Mark Abraham <Mark.Abraham@anu.edu.au><br>> > Subject: Re: [gmx-users] modify bondfree.c and recompile<br>> > To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> > Message-ID: <48FE7A8A.3000704@anu.edu.au><br>> > Content-Type: text/plain; charset=UTF-8; format=flowed<br>> ><br>> > Jian Zou wrote:<br>> >> Hi,<br>> >><br>> >> If I only change some functional form in bondfree.c (the number of<br>> >> parameters are kept the same), can I just do "make mdrun" and "make<br>> >> install-mdrun" to recompile from the source?<br>> >><br>> >> I cannot find the dependency between the source files and the Gromacs<br>> >> utilities (grompp and mdrun).<br>> ><br>> > It's there in the Makefiles, but you don't need to know about it. Just<br>> > use make (or just make mdrun) from the top-level source directory.<br>> ><br>> >> I compare the tpr file generated before and after the change and they<br>> >> are the same. Therefore it seems to me that grompp does not read the<br>> >> formulation of bonded interactions, am I right?<br>> ><br>> > grompp isn't changing, so its output is the same. All it does is<br>> > interpret the contents of your .top file and tell mdrun which function<br>> > to use.<br>> ><br>> > Mark<br>> <br>> <br>> > Message: 5<br>> > Date: Wed, 22 Oct 2008 08:09:17 +0200<br>> > From: David van der Spoel <spoel@xray.bmc.uu.se><br>> > Subject: Re: [gmx-users] modify bondfree.c and recompile<br>> > To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> > Message-ID: <48FEC38D.8060907@xray.bmc.uu.se><br>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>> ><br>> > He, Yang wrote:<br>> >> Hi Jian,<br>> >><br>> >> Do you also need to change the source code to get a new potential function? I am also engaged in this job. DO you have any experience about this job?<br>> >><br>> >><br>> > You can use tables for bonded potentials as well, without changing any code.<br>> ><br>> >> Regards,<br>> >><br>> >> Yang<br>> >> ________________________________________<br>> >> From: gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] On Behalf Of Jian Zou [jianzou@gmail.com]<br>> >> Sent: Tuesday, October 21, 2008 7:24 AM<br>> >> To: gmx-developers@gromacs.org; gmx-users@gromacs.org<br>> >> Subject: [gmx-users] modify bondfree.c and recompile<br>> >><br>> >> Hi,<br>> >><br>> >> If I only change some functional form in bondfree.c (the number of<br>> >> parameters are kept the same), can I just do "make mdrun" and "make<br>> >> install-mdrun" to recompile from the source?<br>> >><br>> >> I cannot find the dependency between the source files and the Gromacs<br>> >> utilities (grompp and mdrun).<br>> >><br>> >> I compare the tpr file generated before and after the change and they<br>> >> are the same. Therefore it seems to me that grompp does not read the<br>> >> formulation of bonded interactions, am I right?<br>> >><br>> >> Thank you very much for the reply.<br>> >><br>> >><br>> >> Regards,<br>> >><br>> >> Jian<br>> >> _______________________________________________<br>> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> >> Please search the archive at http://www.gromacs.org/search before posting!<br>> >> Please don't post (un)subscribe requests to the list. Use the<br>> >> www interface or send it to gmx-users-request@gromacs.org.<br>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> >> _______________________________________________<br>> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> >> Please search the archive at http://www.gromacs.org/search before posting!<br>> >> Please don't post (un)subscribe requests to the list. Use the<br>> >> www interface or send it to gmx-users-request@gromacs.org.<br>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> ><br>> > --<br>> > David.<br>> > ________________________________________________________________________<br>> > David van der Spoel, PhD, Professor of Biology<br>> > Dept. of Cell and Molecular Biology, Uppsala University.<br>> > Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>> > phone: 46 18 471 4205 fax: 46 18 511 755<br>> > spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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