Thanks Tsjerk, that works great! Also your explaination was very clear. I would just like to follow up that what works for me was (2 steps):
trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans I now understand also why the following single step conversion doesn't work, but perhaps this following combination should be disallowed by trjconv or the code should be changed to do the rotation as the last step: trjconv -s a.tpr -f a.xtc -o c.xtc -center tric -ur compact -fit rot+trans -pbc inbox > From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Problem with trjconv centering after fitting > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > Would that be the same? What happened here is that the system was > first fitted. Thus, the system is rotated and any operation concerning > pbc after that point will be screwed up, because the box definition > does not match the system. Solution: first perform all operations > involving pbc, then fit the system. Note that translations are not a > problem, only rotations. An alternative solution would be to have all > routines involving rotation of the frame also rotating the box > definition in that frame in the trajectory. But this requires > modifications in many routines. > > Tsjerk > > On 8/28/06, David van der Spoel <[EMAIL PROTECTED]> wrote: > > [EMAIL PROTECTED] wrote: > > > Starting from a rhombic dodecahedron xtc file, > > > > > > trjconv -fit rot+trans -f a.xtc -s a.tpr -o a_fit.xtc > > > trjconv -center rect -pbc whole -f a_fit.xtc -s a.tpr -o a_fit_cent.xtc > > > > > > Visualization of a.xtc and a_fit.xtc via VMD are as expected. > Nevertheless, > > > a_fit_cent.xtc shows overlapping atoms and regions of zero density. Why > is this? > > > > > > _______________________________________________ > > > 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 > > could this be the same problem as reported here: > > > > http://bugzilla.gromacs.org/show_bug.cgi?id=99 > > > > -- > > 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 > > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > _______________________________________________ > > 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 > > > > > -- > > Tsjerk A. Wassenaar, M.Sc. > Groningen Biomolecular Sciences and Biotechnology Institute (GBB) > Dept. of Biophysical Chemistry > University of Groningen > Nijenborgh 4 > 9747AG Groningen, The Netherlands > +31 50 363 4336 > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > > > End of gmx-users Digest, Vol 28, Issue 81 > ***************************************** > _______________________________________________ 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
