Hi Anamika, It would be good to do some background reading on MD. For this issue, you most likely should read:
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Cheers, Tsjerk On Feb 12, 2008 11:14 AM, Anamika Awasthi <[EMAIL PROTECTED]> wrote: > Dear Gromacs users, > I am beginner in using using GROMACS and MD simulations, Please help > me in solving my problem. > I simulate my protein for 5 ns and after simulations RMSD in C-alpha is > showing a big fluctuation after 3 ns and til 3.5 ns to 4.5 ns its fine and > again its showing fluctuation its till 2.5 nm. Please Tell me how should I > analyze this and How can I sort out this problem. > > Thanking you > > -- > Anamika Awasthi, PhD > DBT-Postdoctoral Fellow > Laboratory of Structural Biology > Centre for DNA Fingerprinting and Diagnostics (CDFD) > ECIL Road, Nacharam > Hyderabad 500 076 > INDIA > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php