[gmx-users] Query for RMSD

[Mark Abraham]

On 01/24/11, Archana Sonawani  <ask.archana at gmail.com> wrote:
> Hello,
> 
>  
> 
> I have run 10 ns simulation for ligand-receptor complex. For analysis, I checked RMSD, Radius of gyration, Hydrogen bonds and distance using g_dist. 
> 
>  
> 
> In the RMSD plot, the whole simulation shows RMSD between 0 - 0.5nm , but after 5ns I get long vertical lines upto 2.5 nm. I dont know whats the reason for that. I am sending the RMSD plot as attachment.
> 
> These lines are not seen in case of hydrogen bond plot and distance plot. Please help me out.
> 
>  
> 
> 
These are almost certainly periodicity artefacts. Look at your trajectory in a suitable visualization algorithm, and you will see (parts of) the complex cross boundaries at those points. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for discussion and solution approaches.

Mark

> 
> 
> 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110124/bb146acc/attachment.html>