Hi James, > 1- Can I obtain same fluctuations along ensemble of several modes (i.e > averaged fluctuations along modes from n to k ) in one graph ?
The total fluctuation is the sum of the fluctuations along all the modes. To get what you want, you just need to some the fluctuations. Alternatively, you can filter a trajectory using a set of modes and do further analysis on that. > 2- Is there any way to obtain fluctuations of C-alpha atoms or backbone only > from full atomic model ? See the answer above. > but I can chose only full atomic representation of the system consisted of > 6518 atoms and any other selection would produce error. > Is there any other way to obtain fluctuations on reduced number of atoms > from full-atomic system ? g_anaeig needs the atoms to match with the eigenvectors, which pertain to the full set of atoms. > 3- Also I've done two different NMA from one reference ( for full atomic > model and for C-alpha mode). > The overal picture of RMSF for instance was overal in both of the analysis > but in case of the C-alpha only ANM RMSF were bigger in 10 times (0.02 Nm in > case of full atomic NMA vs 2 NM in case of C-alpha NMA on equat residues). > Why that difference might occur? Is there any way to increase amplitude of > fluctuations by the temperature rising for instance ? The c-alphas are less hindered in the second model due to the absence of the side chains and such. There's just more freedom. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
