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 /<[email protected]>/* wrote:
From: Tsjerk Wassenaar <[email protected]>
Subject: Re: [gmx-users] -center -fit dodecahedron : dimer
To: "Discussion list for GROMACS users" <[email protected]>
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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