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Feature #1030

adding -tu option to some analysis tools

Added by Francesco Oteri almost 7 years ago. Updated about 3 years ago.

Status:
Fix uploaded
Priority:
Low
Category:
analysis tools
Target version:
-
Difficulty:
uncategorized
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Description

Good morning,
I think it is useful adding the option -tu in g_rmsf.
Nowadays people are simulating for several nanoseconds so
using yet the picosecond notation is, in my opinion, very annoying.
Thank you
Francesco


Related issues

Has duplicate GROMACS - Feature #1029: -tu option in g_rmsfClosed11/05/2012

History

#1 Updated by David van der Spoel almost 7 years ago

What do you mean? g_rmsf gives time averages and no time is printed. Therefore this must be a misunderstanding.

#2 Updated by Justin Lemkul almost 7 years ago

g_rmsf may not be an appropriate example, but several analysis tools have -tu and others lack it. Perhaps more generally, all analysis tools should include this option (where applicable).

#3 Updated by David van der Spoel almost 7 years ago

I don't see any such program where it is missing.

#4 Updated by Francesco Oteri almost 7 years ago

I mean I cannot use nanoseconds to use -b and -e flags.
I'd like to use something like:
g_rmsf -b 30 -e 50 -tu ns .....

It is not a big problem but, since I am trying to write some script
to run analysis. For this lack of uniformity, I've to complicate the
scripts.

#5 Updated by Justin Lemkul almost 7 years ago

Francesco Oteri wrote:

I mean I cannot use nanoseconds to use -b and -e flags.
I'd like to use something like:
g_rmsf -b 30 -e 50 -tu ns .....

It is not a big problem but, since I am trying to write some script
to run analysis. For this lack of uniformity, I've to complicate the
scripts.

All Gromacs trajectories are stored using ps by default. If you want to use ns for everything, you should be able to run trjconv as the first step and reset the units (trjconv -tu ns).

#6 Updated by Roland Schulz almost 7 years ago

Using latest 4.6 the g_rmsf doesn't have -tu whereas e.g. g_rms does. The reason is that g_rmsf doesn't have PCA_TIME_UNIT set. It seems to me that PCA_CAN_TIME should imply PCA_TIME_UNIT.

#7 Updated by Justin Lemkul almost 7 years ago

David van der Spoel wrote:

I don't see any such program where it is missing.

It seems that most analysis tools lack -tu. Those for which it seems like it would make sense to add the -tu option:

g_analyze (don't really know if this makes sense necessarily)
g_angle
g_current
g_dielectric
g_dih
g_dipoles
g_disre
g_dist
g_energy
g_gyrate
g_h2order
g_helix
g_helixorient
g_lie
g_rmsdist
g_saltbr
g_sas
g_sgangle
g_sorient

The following tools I have never used so I'm not sure if they can use -tu:
g_rotacf
g_spol
g_tcaf
g_vanhove
g_velacc

#8 Updated by Erik Lindahl over 5 years ago

  • Tracker changed from Bug to Feature

#9 Updated by Rossen Apostolov over 5 years ago

#10 Updated by Gerrit Code Review Bot over 5 years ago

Gerrit received a related patchset '1' for Issue #1030.
Uploader: Rossen Apostolov ()
Change-Id: I24140464e0e181c465d0b12d38d0c4d41af5cec7
Gerrit URL: https://gerrit.gromacs.org/3541

#11 Updated by Rossen Apostolov over 5 years ago

  • Status changed from New to Fix uploaded
  • Target version set to 5.0

fixed it for 5.0.

#12 Updated by Rossen Apostolov about 5 years ago

  • Subject changed from g_rmsf to adding -tu option to some analysis tools
  • Assignee changed from David van der Spoel to Rossen Apostolov

#14 Updated by Erik Lindahl about 5 years ago

  • Target version changed from 5.0 to 5.x

We realized this is a too large fix to commit last-minute since it affects lots of programs.

#15 Updated by Mark Abraham about 3 years ago

  • Target version deleted (5.x)

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