[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
>>>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?
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
> 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.
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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
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