[gmx-users] g_rms problem

David spoel at xray.bmc.uu.se
Wed Sep 17 14:51:02 CEST 2003

On Wed, 2003-09-17 at 14:00, Dmitry Kovalsky wrote:
> Hi,
> I want to use g_rms to compare a final conformation to an initial one by 
> computing rmsd of their  Ca atoms. It gives me a value of 3A. Visual 
> comparision tells me that this value is too high. I used DeepView to do it 
> again and it gives me a value of 1.6A, which is reasonable. Why g_rms gives 
> high values or tell me what I'm doing wrong.

That's weird... Can you compare the results to g_confrms too?
That is a different implementation of the RMSD. It almost seems like a
sqrt, but in the code the sqrt is in place... 
> Dima 
Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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