Hi, I think after the "trjconv -f *.trr -n deshuf.ndx" operation, the new orders of x and v in the trr file are correct. Here "correct" means the order is the same as the intitial *.gro file you use for grompp command. If the output of trjconv is gro/pdb, you're right that it's only deshuffled, but not desorted. But since there's no force in the gro file, the bug i mentioned is only in the case when you choose trr as the output of your deshuffle operation. Lanyuan Lu ---------------------------------------- > Date: Thu, 24 Jan 2008 12:28:47 -0500 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] deshuf.ndx doesn't work for forces? > >> Message: 2 >> Date: Wed, 23 Jan 2008 18:56:22 -0500 >> From: LuLanyuan >> Subject: [gmx-users] deshuf.ndx doesn't work for forces? >> To: >> Message-ID: >> Content-Type: text/plain; charset="gb2312" >> >> >> Hello All, >> I found sth like a bug regarding the deshuffle index file. I did a >> simulation using multiple cpus and -sort -shuffle options. After >> that I tried to use the deshuf.ndx file to recover the original atom >> order for my trr file by trjconv -n deshuf.ndx ... command. > > As I understand it, the deshuf.ndx file does not allow you to desort, > merely to deshuffle. > >> But by checking the output trr using the gmxdump, I found the oders >> of x and v were deshuffled while the f oder remained unchanged. In >> another word the values of forces were not consistent with those of >> positions and velocities in the new trr file. >> Is this a bug? > > So the order of the positions and velocities has changed, but are they > correct? I do not believe that gromacs 3.3.1 is capable of desorting, > nor is it supported. I have uploaded a tool called g_desort to the > users contribution section. It works well and is tested, but it's > usage is complicated when you want to load in .trr files via grompp. > >> And is there anyway to get the correct oder for forces also? > > I suggest that you try to reproduce this problem while using -shuffle > but not -sort. > >> Thanks a lot. >> Lanyuan Lu >> _________________________________________________________________ > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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
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