[gmx-users] Problem with trjconv centering after fitting

[chris.neale at utoronto.ca]

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" <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Problem with trjconv centering after fitting
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> 	<8ff898150608280234o744f9d97rc0468a958711a620 at mail.gmail.com>
> 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 <spoel at xray.bmc.uu.se> wrote:
> > chris.neale at utoronto.ca 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?
> > >
> > > _______________________________________________
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> > 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
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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> 
> 
> -- 
> 
> 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
> 
> 
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> End of gmx-users Digest, Vol 28, Issue 81
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>