Hi Jia, You can use trjconv for custom fitting, and then feed the fitted trajectory to g_rms, not using fitting there. Either that's using -nofit or -fit none.
Cheers, Tsjerk On Tue, Dec 4, 2012 at 6:06 AM, Jia Xu <[email protected]> wrote: > Dear gromacs users, > I have a trajectory of 500-atom system and would like to obtain RMSD of > all atoms but only aligned to residue 1-400 of a reference structure. Is > there any way to do this? > Thank you so much! > Regards, > Jia > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
