Hi Anirban, If you calculate the RMSD over a trajectory using g_rms and do block averaging on the result, it won't give you any information about convergence. The conformational space away from the reference structure (>0.1nm, >0.5nm?) is just too big. This means that the protein can be moving a lot, without showing in the RMSD.
Cheers, Tsjerk On Mon, Apr 22, 2013 at 12:00 PM, Anirban <[email protected]>wrote: > Hi ALL, > > In order to see the convergence of a trajectory I am trying to calculate > the RMSD error estimate using block averaging method which is implemented > using g_analyze with -ee option. In it can I manually provide the block > size or is it calculated based on the total simulation time? Another thing, > is this method same as the block average RMSD method outlined by Alan > Grossfield in JCTC 2011:7;2464-2472, in order to test convergence of a > trajectory? > Any suggestion is welcome. > > Regards, > > Anirban > -- > 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. -- 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
