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Bug #2544

gmx rmsf does not fix periodicity in reference structure

Added by David van der Spoel 5 months ago. Updated 2 months ago.

Status:
New
Priority:
Normal
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
simple
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Description

If the periodicity in the input molecule that is use for fitting is not correct, the fit will be done on a broken molecule leading to incorrect fluctuations. This likely is a left-over from the time when GROMACS did not write broken molecules.

broken.tpr (592 KB) broken.tpr David van der Spoel, 06/05/2018 02:10 PM
whole.tpr (592 KB) whole.tpr David van der Spoel, 06/05/2018 02:10 PM
ub_traj.pdb (190 KB) ub_traj.pdb David van der Spoel, 06/05/2018 02:10 PM

Related issues

Related to GROMACS - Feature #2545: Should grompp fix periodicity of input files?New

History

#1 Updated by David van der Spoel 5 months ago

To reproduce:

gmx rmsf -f ub_traj.pdb -s broken.tpr -res -o rmsf_broken

gmx rmsf -f ub_traj.pdb -s whole.tpr -res -o rmsf_whole

#2 Updated by Gerrit Code Review Bot 5 months ago

Gerrit received a related patchset '1' for Issue #2544.
Uploader: David van der Spoel ()
Change-Id: gromacs~release-2018~Ic2b70b3ffc4aa87d1f99b97bc323bcf3d59420ab
Gerrit URL: https://gerrit.gromacs.org/7977

#3 Updated by Mark Abraham 4 months ago

  • Related to Feature #2545: Should grompp fix periodicity of input files? added

#4 Updated by Paul Bauer 2 months ago

  • Target version changed from 2018.3 to future

I changed the target version for this, as this involves more general changed to the way the analysis tools work in the end.

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