[gmx-users] Bug in g_rms -> calculate RhoSc ??
nitramus at hypnos.chem.pg.gda.pl
Tue Dec 17 13:42:04 CET 2002
On Mon, 16 Dec 2002, Marc Baaden wrote:
> 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
> 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 ?
> 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?
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