Thank you for your reply. I checked the coordinates of all C-alpha atoms between two .pdb files. They are exactly the same. So I don't understand why g_rms(g_rmsdist) selecting group C-alpha give me high values.
Sincerely yours, Hsin-Lin Erik Marklund wrote > > Hi, > > Since gromos-forcefields are not strictly all-atom forcefields, there > might be a mismatch between atoms in the two structures. > > Best, > > Erik > > 24 aug 2012 kl. 15.35 skrev Hsin-Lin Chiang: > >> Hi, >> >> For example, I have a A.pdb as a initial structure file. >> And I just used pdb2gmx on it to generate another B.pdb file with >> GROMOS96 43a1 as its force filed. >> Then I select C-alpha atoms to calculate RMSD. >> echo 3 | g_rms -f B.pdb -s A.pdb >> I suppose the RMSD value should be 0, but the value is high to about >> 0.5nm. >> Can someone explain for me? >> >> Sincerely yours, >> Hsin-Lin >> >> -- >> gmx-users mailing list gmx-users@ >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Only plain text messages are allowed! >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-request@. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > erikm@.uu > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > gmx-users mailing list gmx-users@ > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request@. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- View this message in context: http://gromacs.5086.n6.nabble.com/g-rms-and-g-rmsdist-on-initial-structure-tp5000492p5000496.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists