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

Sunita Patel sunita at chem.iitb.ac.in
Tue May 11 20:58:35 CEST 2004

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.


Sunita Patel
Biophysical Lab.,
Dept. of Chemistry,
Indian Institute of Technology(IIT) Bombay,
Powai, Mumbai, Maharashtra,

Tel: (91)-22-25764176.
Email:sunita at chem.iitb.ac.in

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