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

[David van der Spoel]

On Tue, 2004-05-11 at 20:58, 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.
It's fine. They are simulating a crystal and hence the crystal contacts
reduce the freedom of the protein to move.
> 
> 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
> -------------------------------------------------------------------------------
> 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++