<div dir="ltr">One more question: How do I get my new g_whatever analysis to be included in the compilation? <br>Simply placing my file in src/tools won't work of course. How to I place it correctly in the build?<br>Thanks,<br>
-Shay<br><br><div class="gmail_quote">2012/6/5 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
On 6/4/12 5:16 PM, Shay Teaching wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
2012/6/4 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div class="im"><br>
<br>
<br>
<br>
On 6/4/12 2:59 PM, Shay Teaching wrote:<br>
<br>
Dear Gromacs users,<br>
<br>
I want to write new analyses for gromacs and compile it (so I'll have<br>
g_whatever) as part of the gromacs package.<br>
Per the instructions I found on gromacs website, I installed kdevelop<br>
and opened<br>
the gromacs as a project using kdevelop. However I have two questions:<br>
1) When I try to compile gromacs source, through kdevelop, I get a<br>
"permission<br>
denied" error. I think it is because gromacs installation requires root<br>
privileges. Any suggestions on how to bypass that, so I won't have to use<br>
kdevelop as root (which is a *really* bad idea)? (e.g., installing gromacs<br>
without root?)<br>
<br>
<br>
Assuming you're trying to compile template.c in some system-level directory,<br>
you're certain to run into that problem. Compile in a different location.<br>
<br>
Actually, I tried installing Gromacs to my home directory, not system directory.<br>
You're saying that I'm not supposed to encounter this error?<br>
<br>
</div></blockquote>
<br>
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?<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
2) Are there any guidelines for writing new g_whatever analyses? Or any<br>
general<br>
suggestions on how to approach it?<br>
<br>
<br>
Write good code? ;) I don't really know what you're asking here, but if you<br>
want pointers for writing code, you'll need to at least state what you're doing.<br>
<br>
Write good code of course :-)<br>
What I mean is: Is there a proper list of gromacs functions used for 'common'<br>
operations? (such as, reading from trajectory, reading index file, documentation<br>
of types and data structures for dealing with gromacs trajectory: atom,<br>
molecule, their input and output, etc.)<br>
Of course I'll open existing analyses, and see how its done there (g_mindist,<br>
g_rms..) but it would be useful to have like... a list of methods so I won't<br>
waste time on stuff that's already been dealt with.<br>
<br>
</blockquote>
<br></div>
The only related information is probably on the website at <a href="http://www.gromacs.org/Developer_Zone/Programming_Guide" target="_blank">http://www.gromacs.org/<u></u>Developer_Zone/Programming_<u></u>Guide</a>. 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.<div class="HOEnZb">
<div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
-- <br>
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