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

Shay Teaching shay.teaching at gmail.com
Mon Jun 4 23:16:39 CEST 2012

2012/6/4 Justin A. Lemkul <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?

>  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>
> ==============================**==========
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