I think you need to add -force option. Like trjconv -f a.trr -force -o b.trr Lanyuan Lu ---------------------------------------- > Date: Thu, 24 Jan 2008 17:39:45 -0500 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] Re: deshuf.ndx doesn't work for forces? > > My apologies, The commands should have been: > > trjconv -f a.trr -o b.trr > gmxdump -f a.trr> a.dump > gmxdump -f b.trr> b.dump > diff a.dump b.dump> ab.diff > > Chris Neale wrote: >> OK, I can confirm this for 3.3.1. However, I don't think that the >> problem is one of shuffling or sorting but simply that >> trjconv -f a.trr -o b.trr creates an exact copy of the .trr file >> *without* the forces. You can easily verify this by doing this: >> >> trjconv -f a.trr -o b.trr >> gmxdump -f a.trr> a.dumo >> gmxdump -f b.trr> b.trr >> diff a.trr b.trr> ab.diff >> >> Note that b.trr is of smaller size then b.trr and the ab.diff file >> clearly shows that it is the forces that are missing. >> >> I actually have never tested that before now so it appears that my >> g_desort routine will lead to the loss of force information at each >> re-sorting event by nature of passing through trjconv -o .trr. >> >> I did take a quick look at the gmx_trjconv code but I am unable to >> determine the particular place where the code might be changed. >> However, I think that I have isolated it to the need to add an output >> of force data from the -o .trr option to trjconv. >> >> Chris >> >> >> >> --- Original Message --- >> >> Hi, >> I think after the "trjconv -f *.trr -n deshuf.ndx" operation, the new >> or= >> ders of x and v in the trr file are correct.=20 >> 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 >> de= >> sorted. 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: chris.neale at utoronto.ca >> >> />/ To: gmx-users at gromacs.org >> >> />/ Subject: [gmx-users] deshuf.ndx doesn't work for forces? >> />/=20 >> />>/ Message: 2 >> />>/ Date: Wed, 23 Jan 2008 18:56:22 -0500 >> />>/ From: LuLanyuan=20 >> />>/ Subject: [gmx-users] deshuf.ndx doesn't work for forces? >> />>/ To:=20 >> />>/ Message-ID:=20 >> />>/ Content-Type: text/plain; charset=3D"gb2312" >> />>/ >> />>/ >> />>/ Hello All, >> />>/ I found sth like a bug regarding the deshuffle index file. I did >> a =20 >> />>/ simulation using multiple cpus and -sort -shuffle options. After >> =20 >> />>/ that I tried to use the deshuf.ndx file to recover the original >> atom =20 >> />>/ order for my trr file by trjconv -n deshuf.ndx ... command. >> />/=20 >> />/ As I understand it, the deshuf.ndx file does not allow you to >> desort, =20 >> />/ merely to deshuffle. >> />/=20 >> />>/ But by checking the output trr using the gmxdump, I found the >> oders =20 >> />>/ of x and v were deshuffled while the f oder remained unchanged. >> In =20 >> />>/ another word the values of forces were not consistent with those >> of =20 >> />>/ positions and velocities in the new trr file. >> />>/ Is this a bug? >> />/=20 >> />/ So the order of the positions and velocities has changed, but are >> they = >> /=20 >>> / correct? I do not believe that gromacs 3.3.1 is capable of >>> desorting, =20 >> />/ nor is it supported. I have uploaded a tool called g_desort to the >> =20 >> />/ users contribution section. It works well and is tested, but it's =20 >> />/ usage is complicated when you want to load in .trr files via grompp. >> />/=20 >> />>/ And is there anyway to get the correct oder for forces also? >> />/=20 >> />/ I suggest that you try to reproduce this problem while using >> -shuffle =20 >> />/ but not -sort. >> />/=20 >> />>/ 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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