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

nahren manuel meetnahren at yahoo.com
Wed Apr 22 11:58:55 CEST 2009


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
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



      
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090422/589c994e/attachment.html>


More information about the gromacs.org_gmx-users mailing list