[gmx-users] -center -fit dodecahedron : dimer
Dear Gromacs Users, I am performing a MD simulation of a dimer in a dodecahedron box. The simulation stopped after 8 ns (power cut) and i had to restart to complete it fully to 12 ns. I then concatenated the two trajectories using trjcat 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. 2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run) I feel I am missing something here. Kindly advice. regards, nahren ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] -center -fit dodecahedron : dimer
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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] -center -fit dodecahedron : dimer
nahren manuel wrote: Dear Gromacs Users, I am performing a MD simulation of a dimer in a dodecahedron box. The simulation stopped after 8 ns (power cut) and i had to restart to complete it fully to 12 ns. I then concatenated the two trajectories using trjcat 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. The last operation fits to a structure, permitting rotations and translations. If the target is not centered in its box... 2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run) I feel I am missing something here. Kindly advice. It's a periodic box - a mathematical construction. The simulation doesn't care where the atoms go in relation to it. If you care, you can apply trjconv afterwards. Mark ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] -center -fit dodecahedron : dimer
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 tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] -center -fit dodecahedron : dimer To: Discussion list for GROMACS users gmx-users@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@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] -center -fit dodecahedron : dimer
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 /tsje...@gmail.com/* wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] -center -fit dodecahedron : dimer To: Discussion list for GROMACS users gmx-users@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 listgmx-users@gromacs.org /mc/compose?to=gmx-us...@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-requ...@gromacs.org /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
