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

[nahren manuel]

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.?

>> 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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