2012/6/4 Justin A. Lemkul <[email protected]> > > > 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? > > > 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. > -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 [email protected] > 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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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