[gmx-users] Is 1.4 A is a large rms incontrast to 0.33 A ?

[Erik Lindahl]

Hi,

Not having the paper at hand, my guess is that the first created  
average structures from the four chains, and then calculated RMSD. Or  
was 0.33 the standard deviation of the RMSD over the four structures?

While 1.4 A (if you mean Angstroms, and not nanometers) is a pretty  
good RMSD for a protein, 0.33 is too low to believe from a simulation  
where all atoms are free to move... That's almost as low as an NMR  
structure, which already is an average over time and molecules.

Cheers,

Erik





On May 11, 2004, at 8:58 PM, Sunita Patel wrote:

> Dear gmx_users,
>
> I am trying to reproduce the rmsd deviation (0.33 A) as reported in the
> article PNAS, 1994, 91, 8715-8718. For all-atom MD simulation they  
> have used
> AMBER forcefield with explicit TIP3P water and PME for electrostatic
> interaction. Their unit cell has 4 monomers of the same BPTI protein.
>
> But I am using GROMOS96 forcefield with explicit spc water and PME for
> long range electrostatic interaction. But instead of 4 monomers I am  
> using
> a single protein. The RMSD value I am getting is quite surprising. It  
> is
> 1.4 A.
>
> The protocol which I am using, seems to be ok or this rmsd is a
> significant difference.
>
> Thanks for any suggesstion.
>
> Regards,
> Sunita
>
> ----------------------------------------------------------------------- 
> --------
> Sunita Patel
> Biophysical Lab.,
> Dept. of Chemistry,
> Indian Institute of Technology(IIT) Bombay,
> Powai, Mumbai, Maharashtra,
> INDIA-400076.
>
> Tel: (91)-22-25764176.
> Email:sunita at chem.iitb.ac.in
> ----------------------------------------------------------------------- 
> --------
>
>
>
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