[gmx-users] SHUFFLING tutorial

[Jason DeJoannis]

Hi,

 This won't solve your problem but since we are on
the subject of deshuffling things... here is a script
I use to deshuffle .gro files or even to extract groups
from .gro files etc. Maybe some of you can use it.

Jason

---
Jason de Joannis, Ph.D.
Chemistry Department, Emory University
1515 Pierce Dr. NE, Atlanta, GA 30322
Phone: (404) 712-2983
Email: jdejoan at emory.edu
http://userwww.service.emory.edu/~jdejoan



Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> On Tue, 2003-04-29 at 04:26, Dallas Warren wrote:
> > I have a trajectory in which the shuffle/sort option has been used (and I 
> > don't use this anymore since it did improve scaling very much and the 
> > problems in subsequent analysis of the files).  Now I am trying to analyze
> 
> > it using g_sas.
> > 
> > Using the trajectory file as it is written out and the topology file used 
> > as the input to generate that trajectory, I get a segmentation fault.
> > 
> > If the trajectory is then deshuffled using the deshuffle index file 
> > generated by grompp when the topology file is generated, then the warning 
> > about inconsistency shifts etc appears, which isn't surprising since the 
> > topology file is still shuffled.
> > 
> > I found a couple of previous discussions on the analysis of shuffled 
> > trajectories, but all has been said is that you can deshuffle using the 
> > deshuffle index file generated.  Also, someone did ask if you had to also 
> > generate a deshuffled topology file and it appears that you 
> > don't.  Additionally, you should be able to use a shuffled index file.
> > 
> > I attempted to generate a deshuffled gro file to then use to produced a 
> > deshuffled index file to use, however editconf gives a segmentation fault.
> > 
> > Am I missing something here, or is it not possible for me to analyse this 
> > trajectory?
> > 
> I went through this hassle just recently myself, and it turns out that
> the deshuf.ndx generated by grompp is just an evil mixture of "old" and
> "new" index files. At some stage we decided to change the format of the
> index file to be more "user friendly". All the programs can still read
> both files, but they have to be internally consistent. Problems arise
> because the old format started counting at 0, while the new starts
> counting at 1. Here's what to do:
> 
> If your standard dsehuf.ndx for a system of N atoms starts with:
> [ deshuf ]
> 0 1 4 6 7 etc.
> you have to modify it to the old format:
> 1 N
> deshuf N
> 0 1 4 6 7 etc.
> 
> You only have to change the top bit, not the actual numbers. An
> alternative is to modify it to be:
> [ deshuf ]
> 1 2 5 7 8 etc.
> 
> That wouldn't be too hard with a script either.
> 
> OK, now you have a proper deshuf.ndx, time to run trjconv etc.
> 
> trjconv -f traj.xtc -n deshuf -o deshuf.xtc
> trjconv -f traj.trr -n deshuf -o deshuf.trr
> editconf -f confout.gro -n deshuf -o deshuf.gro
> 
> Finally, you *will* have to create a normal topology with grompp for
> analysis tools. There may be some programs that don't read the tpr, but
> take no chances. It can get really messy with programs reading the file
> without you noticing and produce incorrect results. g_sas is a good
> example, it will happily create nonsensical numbers if your coordinates
> are shuffled.
> 
> 
> -- 
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: deshuffle
Type: application/octet-stream
Size: 1220 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20030429/cf5906d0/attachment.obj>