One more question: How do I get my new g_whatever analysis to be included in the compilation? Simply placing my file in src/tools won't work of course. How to I place it correctly in the build? Thanks, -Shay
2012/6/5 Justin A. Lemkul <jalem...@vt.edu> > > > On 6/4/12 5:16 PM, Shay Teaching wrote: > >> >> >> 2012/6/4 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> >> >> >> >> On 6/4/12 2:59 PM, Shay Teaching wrote: >> >> Dear Gromacs users, >> >> I want to write new analyses for gromacs and compile it (so I'll >> have >> g_whatever) as part of the gromacs package. >> Per the instructions I found on gromacs website, I installed >> kdevelop >> and opened >> the gromacs as a project using kdevelop. However I have two >> questions: >> 1) When I try to compile gromacs source, through kdevelop, I get a >> "permission >> denied" error. I think it is because gromacs installation requires >> root >> privileges. Any suggestions on how to bypass that, so I won't have >> to use >> kdevelop as root (which is a *really* bad idea)? (e.g., installing >> gromacs >> without root?) >> >> >> Assuming you're trying to compile template.c in some system-level >> directory, >> you're certain to run into that problem. Compile in a different >> location. >> >> Actually, I tried installing Gromacs to my home directory, not system >> directory. >> You're saying that I'm not supposed to encounter this error? >> >> > You shouldn't have permission errors in your home directory. I've never > used KDevelop; what happens if you try to compile from a normal command > line? > > > >> >> 2) Are there any guidelines for writing new g_whatever analyses? >> Or any >> general >> suggestions on how to approach it? >> >> >> Write good code? ;) I don't really know what you're asking here, but >> if you >> want pointers for writing code, you'll need to at least state what >> you're doing. >> >> Write good code of course :-) >> What I mean is: Is there a proper list of gromacs functions used for >> 'common' >> operations? (such as, reading from trajectory, reading index file, >> documentation >> of types and data structures for dealing with gromacs trajectory: atom, >> molecule, their input and output, etc.) >> Of course I'll open existing analyses, and see how its done there >> (g_mindist, >> g_rms..) but it would be useful to have like... a list of methods so I >> won't >> waste time on stuff that's already been dealt with. >> >> > The only related information is probably on the website at > http://www.gromacs.org/**Developer_Zone/Programming_**Guide<http://www.gromacs.org/Developer_Zone/Programming_Guide>. > I doubt you'll get a how-to for coding though. The approach of looking at > existing files for these routines is probably as efficient as it gets. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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