[gmx-users] g_rms problem
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:
> 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...
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
More information about the gromacs.org_gmx-users