Like Yang Ye said, molecule is likely out of the box (just fix PBC). This also happens when you don't know how to continue a broken simulation (check the WIKI on gmx website) I had this PBC issue many times. What works over here to make things easier is:
Be sure that in the reference frame "-s" the molecule is in the box. 1) remove pbc trjconv -s md.tpr -f md.xtc -o md.nojump.xtc -pbc nojump (also remove water since you don't need them for g_rms) 2) check with "vmd" to see if it worked 3) fit the trajectory ( and keep for animations :) ) trjconv -s md.tpr -f md.nojump.xtc -o md.nojump.fit.xtc -fit rot+trans 4) check the result with "vmd", it looks beautiful 5) g_rms -f md.nojump.fit.xtc ..... Have fun, Diego Enry. On Wed, Jun 18, 2008 at 2:55 AM, Yang Ye <[EMAIL PROTECTED]> wrote: > Quite likely, it is due to part of molecule moving "out of box". Also, the > molecule could be of multiple chain. > > So you need to find a way to put the whole molecule in one piece. Try > various options from trjconv -pbc. If it is DNA, a trick is to define one > chain as an index group and then center that group. > > Regards, > Yang Ye > > Anamika Awasthi wrote: >> >> >> Dear All, >> Please tell, what should I predict from this graph? >> I can understand this is normal type of graph. >> Sorry for inconvenience, but I want to ask some questions, >> my this job crashed many time, because of power shut down and I had to >> restart this again and again, I used tpbconv for the same. >> but now when I was trying to get rmsd plot from my running job..its not >> reading the tpr file, which I got from tpbconv , its reading previous tpr >> file. >> Is it okey? >> Thanks in advance >> Anamika >> >> >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
