[gmx-users] RMSD of MD run

[David van der Spoel]

On Thu, 2003-11-06 at 10:33, Ran Friedman wrote:
> Hi, 
> 
> I've made a 3ns  md run of a system consisting a protein, a small
> ligand, water and some salt molecules. 
> The backbone RMSD of the protein was stable during the first 2ns, with
> a maximum value of 1.8nm. Most of the time the RMSD was ~1.5nm. 
> After ~2ns, the RMSD started rising. It reached ~1.95ns at 3ns. 

> My question is: 
> 1. Does this necessarily means that there's something wrong with my
> simulation? 
> 2. If it doesn't, how can I verify it (i.e. how can I make sure that
> the protein undergoes a some kind of a conformational change)? 
> 

Are you sure it's 1.5 nm? That sounds ridiculously high. Otherwise I've
seen conformational changes happen after 50 ns, so anything is
possible...


> I'd appreciate any help, 
> Ran. 
> -- 
> ------------------------------------------------------
> Ran Friedman
> Laser laboratory for fast reactions in biology
> Department of biochemistry
> Faculty of life sciences
> Tel-Aviv university
> 972-3-6409824
> ------------------------------------------------------
>  
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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