Hi Steve, Did you try a plain -fit rot+trans in trjconv. That should remove both com translation as well as rotation. Select the 'protein' group for the least squares fit.
On Tue, May 27, 2014 at 1:09 AM, Steve Seibold <steve...@ymail.com> wrote: > I REALLY need some help here. I have tried for several days now and looked > on line to fix the situation. My protein moves around and goes outside the > simulation waterbox and my Zinc ions also frequently have bonds to protein > of 40 angstroms are so. > > Here is one of the combinations I have tried so far to remove > translational motion of protein and keep it in the center of the box: > > trajconv -f pr13.trr ( traj. file containing the last 8 ps) -s pr1.tpr > (containing the first pdb structure before any MD, but with waters etc) > -pbc atoms (place all atoms into center of box) -center -boxcenter tric -o > protein13.trr > > This results in protein no longer separating into parts (pieces), but > protein moves, still all over the box and outside of the box..and Zincs > still have long bonds... > > > Then, I use 'fit' as follows in an attempt to do a least squares fit of > all trajectories (positions) back onto initial structure which is in center > of box..... > > > trajconv -s pr1.tpr -f protein13.trr (using the output from above) -fit > progressive -o protein13A.trr > > This didn't help at all.. > > I am really at a loss here on how to deal with this and could use some > help.. > > Steve > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.