Project

General

Profile

Bug #523

g_rms gives nonsense values when the number of atoms differs between tpr and xtc

Added by David van der Spoel over 9 years ago. Updated over 9 years ago.

Status:
Closed
Priority:
Normal
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

If the number of atoms in tpr is less than xtc, g_rms will generate larger RMS values than correct. Some initialization problem in the xp array is to blame I think.

History

#1 Updated by Berk Hess over 9 years ago

Did you really mean that the number of atoms in the tpr is less than in the xtc?
That should simply not be allowed by g_rms.

Berk

#2 Updated by David van der Spoel over 9 years ago

The specific case was a protein complex where I wanted to do an RMSD of the protein in the complex with respect to a pdb/tpr file. At the minimum, g_rms should not generate incorrect values but it would be better to be able to compare trajectories to different other files (e.g. when comparing to homologues).

#3 Updated by Berk Hess over 9 years ago

I think this was a matter of correcting the atom counts.
We should not use natoms>top.atoms.nr.
Please try the fix I committed (also for natoms==top.atoms.nr
and natoms<top.atoms.nr), since I did not test anything.

Berk

#4 Updated by Erik Lindahl over 9 years ago

Works for my small test system and produces identical results.

Also available in: Atom PDF