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Bug #523

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

Added by David van der Spoel almost 10 years ago. Updated almost 10 years ago.

Status:
Closed
Priority:
Normal
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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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 almost 10 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 almost 10 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 almost 10 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 almost 10 years ago

Works for my small test system and produces identical results.

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