[gmx-users] Re: g_rms problem

Dmitry Kovalsky dikov at imbg.org.ua
Thu Sep 18 16:34:01 CEST 2003

Hi David,

Thanks for the advice.
Yes, g_confrms helped me, and the RMSD values became closer enough to that of 
DeepView (however differ in third digit).

How I can get a xvg plot of RMSD not using g_rms?


P.S. May be this bug should be fixed in future? Or it is not a bug?

On Thursday 18 September 2003 09:52, gmx-users-request at gromacs.org 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

Sincerely yours,

Ph.D. Student Dmytro Kovalskyy
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143

E-mail: dikov at imbg.org.ua
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589

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