[gmx-users] -center -fit dodecahedron : dimer

[Mark Abraham]

nahren manuel wrote:
> Dear Gormacs User,
> 
> I have now created a new tpr in which the protein is centered.
> trjconv -f promd.xtc -s tprdodecasolv.tpr -center -boxcenter tric -pbc 
> mol -ur compact -o center.xtc
> trjconv  -s tprdodecasolv.tpr -fit rot+trans -f center.xtc -o fit.xtc
> 
> I see the dimer getting split in some of the frames of fit.xtc.?

You're centering on some group, then allowing translations to fit to a 
structure that might have some different center. So there's no great 
suprise that the result need not be centered. Re-think the order of your 
operations.

Mark

>  >> 2. The box seems to shift from one corner to the center. Especially 
> for the
>  >> duration 8-12 ns (my restart run)
> 
>  >What do you mean with this?
> 
> I actually see my dodeca box jumping from one end of the viewer to 
> another ( in VMD as well as in ngmx)
> 
> thanks for your attention and reply.
> 
> regards
> nahren
> 
> 
> --- On *Wed, 4/22/09, Tsjerk Wassenaar /<tsjerkw at gmail.com>/* wrote:
> 
> 
>     From: Tsjerk Wassenaar <tsjerkw at gmail.com>
>     Subject: Re: [gmx-users] -center -fit dodecahedron : dimer
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Wednesday, April 22, 2009, 2:50 PM
> 
>     Hi Nahren,
> 
>      > trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc
>      > trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center
>     -boxcenter tric -o center.xtc
>      > trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc
> 
>      > 1. The above procedures does not center the molecule in the box.
> 
>     You first center and then do a fit. The fitted trajectory will only be
>     centered if the reference (proem.tpr) is (and then you can skip the
>     second step anyway).
> 
>      > 2. The box seems to shift from one corner to the center.
>     Especially for the
>      > duration 8-12 ns (my restart run)
> 
>     What do you mean with this?
> 
>     Cheers,
> 
>     Tsjerk
> 
> 
>     -- 
>     Tsjerk A. Wassenaar, Ph.D.
>     Junior UD (post-doc)
>     Biomolecular NMR, Bijvoet Center
>     Utrecht University
>     Padualaan 8
>     3584 CH Utrecht
>     The Netherlands
>     P: +31-30-2539931
>     F: +31-30-2537623
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