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
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David.
________________________________________________________________________
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
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