[gmx-users] Re: g_desort

[Chris Neale]

Dear Jennifer:

The line that worries me the most is: "I don't really want to try to 
figure out why gromacs-3.3.2 isn't working". First, I assume that you 
ran your mdrun under gmx-3.3.2 and I would think that you need to 
thoroughly understand why (and more importantly when) it broke. I may or 
may not understand that point, but hopefully it will get cleared up in 
question 2, below.

I have a number of questions. I find that it can get confusing to ask 
many at once, but there are a lot of things that I don't understand, so 
here goes. It would be best for me if you can stick to direct answers of 
each question.

1. I tried again to obtain the tarball from 
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software 
and obtained the same error. Can you obtain the tarball from there now? 
If not, then please send me via personal email the tarball that you 
obtained.

2. You say "..but put it in the dir for gromacs-3.3.2 (not working) and 
not the dir for gromacs-3.3 (working version)"... and then later... "I 
don't really want to try to figure out why gromacs-3.3.2 isn't working" 
-------------------- what does this mean?

2a. Does your main compilation of gmx 3.3.2 work (i.e. can you run 
grompp, mdrun, etc.)?

2b. Does g_desort compile without error when you compile it under 
gromace-3.3 ?

3. You say that you have already generated the trajectories but that you 
were never able to get g_desort to work? Can you confirm this? Sounds 
strange to me because in my opion the -sort option to mdrun gromacs 3 
was entirely useless without the g_desort program. This is because the 
speedup that you see with -sort quickly disappears (the waters migrate 
over space but their home cpu is not modified).

Chris.

-- original message --

Jennifer Rendell wrote:
> Dear Chris,
>
> Thanks for your quick and thoughtful reply. Here are some answers to 
> your questions:
>
> 1.  Info from you found at 
> http://www.mail-archive.com/gmx-users@gromacs.org/msg05351.html
>
> 2.  I got the tarball from 
> http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software. 
> I saved it and opened it up fine.
>
> 3.  I made the Makefile as per your instructions in the README file, 
> but put it in the dir for gromacs-3.3.2 (not working) and not the dir 
> for gromacs-3.3 (working version).
>
> I moved everything to the  
> /usr/local/gromacs-3.3/share/gromacs/template dir and remade the 
> Makefile (no longer has the malaign-double flag set). But I still got 
> the 271 lines of errors of the type I emailed earlier.
>
> 4.  I looked at the file g_desort.c and checked the lines after
> static char *desc[] = {
> It was all comment lines, each with a , at the end. The closing 
> bracket had a }; as did all other lines of similar format.
>
> 5.  We are trying to analyse runs made with gromacs-3.3.2, so I kind 
> of need to work with what I have. I will talk to our users (who aren't 
> here now) to see what they did with this problem...
>
> I appreciate that you don't recall the details on g_desort, and that 
> you are attempting help! I think at the moment I will play around with 
> the gro and trr files and see what I can figure out. I don't really 
> want to try to figure out why gromacs-3.3.2 isn't working. We will 
> install and use gromacs 4.x in the future.
>
> I'll email again if I really can't get anywhere...
>
> Sincerely, Jennifer
>