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Bug #1608

g_velacc g_dos do not match

Added by Yao x over 2 years ago. Updated almost 2 years ago.

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

Dear all,

there are several issues with g_dos and g_velacc.

1. they both do not accept "-n" as they should;

2. g_dos does not accept "-normalize";

3. The output of g_velacc, i.e. -o vel.xvg -os spec1.xvg
do not match that of g_dos, i.e. -vacf vel.xvg -dos spec.xvg, respectively;

4. The g_dos .log file has some errors.

gdos_spec.xvg (35 KB) Yao x, 09/29/2014 03:32 PM

gdos_vacf.xvg (35.9 KB) Yao x, 09/29/2014 03:32 PM

gvelacc_spec.xvg (17.2 KB) Yao x, 09/29/2014 03:32 PM

gvelacc_vacf.xvg (34.1 KB) Yao x, 09/29/2014 03:32 PM

Associated revisions

Revision d51fdb5b (diff)
Added by Erik Lindahl almost 2 years ago

Fix bugs in gmx dos

- Velocity autocorrelations were not normalized
by default, so they did not agree with gmx velacc.
- The normalize option had no effect on the VACs.
- The index group option was available, but no
index groups were processed.
- Since the DoS is calculated from the mass-weighted
VAC and by default only from the real part, it was
not clear why these results would differ from data
obtained with gmx velacc. There is at least a note
about this now, and more docs will be added in the
future.
- The hidden option to dump some plots has been
removed since it was not documented what these
contained (beyond a paper reference), and the
contents was not based on any data from the
trajectory, but rather plotting a custom function.

Fixes #1608.

Change-Id: Icfca060f94efb34bd7871bd90245ab0ddbbe91c1

History

#1 Updated by Yao x over 2 years ago

I use a 2 fs integration step for a typical protein-water binary system.

#2 Updated by Gerrit Code Review Bot almost 2 years ago

Gerrit received a related patchset '1' for Issue #1608.
Uploader: Erik Lindahl ()
Change-Id: I83a9613b6bb051b0fbe969237b9b7979fff0ce04
Gerrit URL: https://gerrit.gromacs.org/4781

#3 Updated by Erik Lindahl almost 2 years ago

  • Status changed from New to Fix uploaded
  • Target version set to 5.0.6

The density-of-states tool appears to have been largely abandoned, and since it also produces velocity autocorrelations that do not agree with those of gmx velacc we should remove it until somebody wants to look into the tool and provide documentation and fixes.

#4 Updated by Gerrit Code Review Bot almost 2 years ago

Gerrit received a related patchset '1' for Issue #1608.
Uploader: Erik Lindahl ()
Change-Id: Icfca060f94efb34bd7871bd90245ab0ddbbe91c1
Gerrit URL: https://gerrit.gromacs.org/4786

#5 Updated by David van der Spoel almost 2 years ago

The -n option does not make sense for gmx dos. I will look into the difference between gmx dos and gmx velacc, but much is probably implemented in patch https://gerrit.gromacs.org/#/c/3175/ already.

#6 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Fix uploaded to Resolved
  • % Done changed from 0 to 100

#7 Updated by Rossen Apostolov almost 2 years ago

  • Status changed from Resolved to Closed

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