[gmx-users] Deshuffling atoms vs. residues

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 1 19:42:25 CEST 2006

Jerome Henin wrote:
> On Tuesday 01 August 2006 10:08, David van der Spoel wrote:
>>Jerome Henin wrote:
>>>Okay, now I have a partial answer to my own question. Apparently, when
>>>using the -sort and -shuffle options, the indexfile written by grompp
>>>undoes the shuffling, but not the sorting, so to speak. This became clear
>>>when I noticed that using just -shuffle without -sort produced the very
>>>same indexfile.
>>>So let me replace my original question with two and a half questions:
>>>1) Is this the intended behavior, and if so, what's the idea behind it?
>>Yes, performance.
I mean performance in mdrun. The not-working index files is due to lack 
of time (and interest) for this feature. This will be supoerfluous in 
4.0 anyway.

> I am not sure I am getting this. What impact does is there on performance, 
> whether the 'deshuffle' index file restores the original residue order or 
> not? Is the problem having to sort residues again for each run in a series?
>>>2) How can I restore the original order?
>>Somehow sort your original file and get a desort.ndx from that, but
>>there is no gromacs tool for that I'm afraid.
> All right, I have written a VMD script that does it. If anyone is interested, 
> I will be glad to provide it.
That's great maybe you can upload it on hte contrib page on the website.
Thanks in advance.

> Jerome
> _______________________________________________
> 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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list