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Bug #2668

gmx anaeig entropy output are not consistent between runs

Added by Magnus Lundborg 7 months ago. Updated 5 months ago.

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

The entropy results I'm getting from anaeig are not consistent.

In this case I'm have a molecule/ligand in solution. When running gmx covar I'm fitting the ligand and using it for covariance analysis.

gmx covar -f ../../equil/equil.xtc -s topol_no_restr_0.tpr -b 1000

That might be right or wrong. However, the results from anaeig is confusing. I'm running:

~/install/gromacs_debug/bin/gmx anaeig -v eigenvec.trr -s topol_no_restr_0.tpr -entropy

If I run it repeatedly with the same input I get:
The Entropy due to the Schlitter formula is 1848.75 J/mol K
The Entropy due to the Schlitter formula is nan J/mol K
The Entropy due to the Schlitter formula is nan J/mol K
The Entropy due to the Schlitter formula is 3156.24 J/mol K
The Entropy due to the Schlitter formula is 1848.75 J/mol K

eigenvec.trr (63.6 KB) eigenvec.trr Magnus Lundborg, 10/04/2018 09:39 AM
covar.log (791 Bytes) covar.log Magnus Lundborg, 10/04/2018 09:39 AM
eigenval.xvg (2.66 KB) eigenval.xvg Magnus Lundborg, 10/04/2018 09:39 AM
topol_no_restr_0.tpr (420 KB) topol_no_restr_0.tpr Magnus Lundborg, 10/04/2018 09:39 AM

Associated revisions

Revision 1538aaba (diff)
Added by David van der Spoel 5 months ago

Fix entropy calculation in gmx anaeig

gmx anaeig reads eigenvectors produced by gmx covar and
can compute entropy according to Schlitter's formula or
based on the quasiharmonic method. If the number of
eigenvectors is not consistent with the number of atoms
the entropy calculation could use uninitialized variables.
Added a warning when this happens.

Fixes #2668

Change-Id: I4f265212ce0a7bf82e25e1aa6f9cbb544c45db3f

History

#1 Updated by David van der Spoel 7 months ago

Can you please upload an example?

#2 Updated by Magnus Lundborg 7 months ago

I'm not uploading the .xtc file. I could do that if needed.

#3 Updated by Magnus Lundborg 6 months ago

  • Target version changed from 2019 to 2020

#4 Updated by David van der Spoel 5 months ago

The tpr file is from master so I can not use it with 2018.

#5 Updated by David van der Spoel 5 months ago

In addition the tpr files is for 15230 atoms while the eigenvec.trr is for 49 atoms.

#6 Updated by Gerrit Code Review Bot 5 months ago

Gerrit received a related patchset '1' for Issue #2668.
Uploader: David van der Spoel ()
Change-Id: gromacs~release-2018~I4f265212ce0a7bf82e25e1aa6f9cbb544c45db3f
Gerrit URL: https://gerrit.gromacs.org/8680

#7 Updated by David van der Spoel 5 months ago

  • Status changed from New to Fix uploaded

Ok the tpr is not needed, however there still is something fishy:

gmx_mpi_d anaeig -f eigenvec.trr -entropy

Read non mass weighted reference structure with 49 atoms from eigenvec.trr
Read non mass weighted average/minimum structure with 49 atoms from eigenvec.trr
Read 90 eigenvectors (for 49 atoms)

The code assumes there should be 3 x 49 = 147 eigenvectors, but there are only 90.

#8 Updated by David van der Spoel 5 months ago

  • Status changed from Fix uploaded to Resolved

#9 Updated by David van der Spoel 5 months ago

  • Status changed from Resolved to Closed

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