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? 2) How can I restore the original order? Thanks, Jerome On Monday 31 July 2006 14:42, Jerome Henin wrote: > Hi, > > I suspect this might be a stupid question, but we've all been beginners one > day, haven't we? > > I have generated a shuffled/sorted trajectory (grompp -sort -shuffle) of a > lipid bilayer, which I have then deshuffled using trajconv and the index > file. In the resulting file, each residue is in one piece again, but the > order of residues seems to be still different from the original one. > Do you have an idea why this happens? > > Thanks a lot, > Jerome _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
