[gmx-users] Bug in g_rms -> calculate RhoSc ??

[Marcin Wojciechowski]

On Mon, 16 Dec 2002, Marc Baaden wrote:

> 
> Hi,
> 
> I was trying to use the alternative similarity measures Rho
> and Rho Scaled from the Crippen and Maiorov paper. Rho looks
> fine, but Rho scaled doesn't make sense, in the way that it
> even looks like a bug to me ..
> 
> So I have put some examples at
> http://indigo1.biop.ox.ac.uk/mbtemp/
> 
> called
> rho.png      - that looks ok/reasonable to me
> rhosc1.png   - a closeup of the problem, a kind of staircase effect 
> rhosc2.png   - same scale as for rho .. that doesn't look right
> rhosc3.png   - not quite as close as rhosc1
> 
> am I talking rubbish ? or can anyone with experience in Rho/Rhosc
> confirm that it is a bug ?
> 
> Cheers,
>   Marc
> 
> -- 
>  Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
>  mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
>  FAX/Voice +49 697912 39550  -  Tel: +44 1865 275380  or  +33 609 843217
> 
> 
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   I havent't tried that, but if we speak about possible bug in g_rms
then i've experienced problems with -skip option. I had a 1ns xtc
trajectory file with 1ps writing frequency and wanted to take structures
to compare every 10ps. G_rms was ignoring the -skip settings and keeping
comparing every step. I had to use trjconv first, generate "skipped xtc"
and then run g_rms.

Could it be a bug in the code?

Regards, MArtin.