[gmx-users] Writing and compiling new analyses for gromacs

[Justin A. Lemkul]

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

-- 
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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

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