Hi Carla, You'll have to use index groups to extract a trajectory and reference that correspond. If you have those you can get on with the RMSD.
Cheers, Tsjerk On Mon, Mar 8, 2010 at 11:44 AM, Carla Jamous <carlajam...@gmail.com> wrote: > Hi everyone, please I just need a precision: > > I need to calculate the RMSD of a trajectory by comparing it to a reference > structure that doesn't have the same number of atoms. > Gromacs is calculating the RMSD, but meanwhile it generates this > warning:"topology has 4839 atoms, whereas trajectory has 4834" > > Does it really affect the result of my RMSD or can I ignore it? > > Thanks > Carla > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.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 > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.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
