[gmx-users] Re: RMSD of MD run

[Spiwok Vojtech]

> I'm sorry - that was a typo. All vlaues should be in Angstroms. 

It is OK.
In my opinion also relatively high RMSD is OK if you can expect
flexibility in a given part of protein, if it makes sense. Other
important parameter is resolution of the initial strucutre, see:
Fan H, Mark AE:
Relative stability of protein structures determined by X-ray
crystallography or NMR spectroscopy: a molecular dynamics
simulation study. Proteins. 2003 Oct 1;53(1):111-20.

Vojtech Spiwok
ICT Prague

> 
> Ran. 
> 
> David van der Spoel wrote: 
> > 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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> -- 
> ------------------------------------------------------
> Ran Friedman
> Laser laboratory for fast reactions in biology
> Department of biochemistry
> Faculty of life sciences
> Tel-Aviv university
> 972-3-6409824
> ------------------------------------------------------
>  

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