[gmx-users] Re: g_rms problem
spoel at xray.bmc.uu.se
Thu Sep 18 16:40:01 CEST 2003
On Thu, 2003-09-18 at 16:33, Dmitry Kovalsky wrote:
> 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?
<Absolutely, however, could this be a matter of options? g_rms now has
lots of confusing options about different fitting mehods, as well as
different things to compute apart from the RMSD... Could you please
check the options?
> 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
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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