[gmx-users] Writing and compiling new analyses for gromacs
Justin A. Lemkul
jalemkul at vt.edu
Mon Jun 4 23:23:10 CEST 2012
On 6/4/12 5:16 PM, Shay Teaching wrote:
> 2012/6/4 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at 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
> 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
> 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. 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users