[gmx-users] Hello

[Tsjerk Wassenaar]

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 <aawasthi28 at gmail.com> 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
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-- 
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