[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
>         "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.  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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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