[gmx-users] Writing and compiling new analyses for gromacs
shay.teaching at gmail.com
Tue Jun 5 00:06:50 CEST 2012
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
>> g_whatever) as part of the gromacs package.
>> Per the instructions I found on gromacs website, I installed
>> and opened
>> the gromacs as a project using kdevelop. However I have two
>> 1) When I try to compile gromacs source, through kdevelop, I get a
>> denied" error. I think it is because gromacs installation requires
>> 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
>> without root?)
>> Assuming you're trying to compile template.c in some system-level
>> you're certain to run into that problem. Compile in a different
>> Actually, I tried installing Gromacs to my home directory, not system
>> 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
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
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
>> 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
>> operations? (such as, reading from trajectory, reading index file,
>> 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_rms..) but it would be useful to have like... a list of methods so I
>> waste time on stuff that's already been dealt with.
> The only related information is probably on the website at
> 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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