[gmx-users] RE:RMSD of MD run (Ran Friedman)

[Spiwok Vojtech]

> 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?

I can imagine 1.8 nm RMSD for some protein which consist of several
domains conected by flexible chains with small contact between domains
(I think antibody could be case) or some snake-shaped protein. Then
it would be more reasonable to do RMSD for each domain or for a domain
of interrest. But 1.8 nm RMSD is big anyway. Isn't it in Angstroms? 

> 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)?

check VMD - http://www.ks.uiuc.edu/Research/vmd/

>
> I'd appreciate any help,
> Ran.
>

Vojtevh Spiwok
ICT Prague
Czech Republic

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