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

[Shay Teaching]

2012/6/5 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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?

It seems you and Peter C. are correct. Kdevelop does not run ./configure.
Knowing that, I executed ./configure manually, but out of habit I did it
using *sudo*. Once I retried without *sudo* everything compiled normally
and correctly.
Out of curiosity - what compiler are you using for gromacs?
Thanks everyone for your quick replies.

>
>
>
>>
>>        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<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
>
> --
> ==============================**==========
>
> 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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