[gmx-users] Hello

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 12 12:06:06 CET 2008

Quoting Anamika Awasthi <aawasthi28 at gmail.com>:

> 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.

There are a few things you can do to help us help you.  This message does not
provide much useful information.

1. Provide an appropriate subject for your email to draw the attention of
someone who might be interested.

2. Describe your system.  I would not be surprised if you get strange results
from simulating a protein at 800K, using a broken topology.  So what is it that
you are doing?  Did grompp give you any error messages that you conveniently
ignored?  It might also be helpful to show us your .mdp file.

When posting to a list like this one, try to be as explicit as possible.  If you
a get a strange result, and that's all you tell us, we can only guess wildly at
the problem.  Also, as a general reference for a newcomer to Gromacs and MD,
have a look at:



>    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


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list