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 <[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 _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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