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Bug #1179

update cut-off treatment checks and documentation, especially PME-switch

Added by Berk Hess over 4 years ago. Updated over 3 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
4.6.1
Affected version:
Difficulty:
uncategorized
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Description

grompp still advises to use PME-switch when running NVE simulations. But PME-switch is deprecated, as we now have exact cut-off's with the Verlet scheme and they can also be used with the group scheme. The confusing effect of the potential-modifier on the cut-off behavior with the group scheme is not reflected in the grompp warnings and mdp-opt.html.

Associated revisions

Revision f78f0dc8 (diff)
Added by Mark Abraham about 4 years ago

Updated grompp cut-off and PME-Switch checks

Added a warning with PME-Switch when switching over more than 5%.
Charge-group size rlist notes/warnings now also appear when
potential modifiers are used.
Documented effect of potential-modifiers on the group scheme cut-off
treatment in mdp_opt.html.

Fixes #1179

Change-Id: Ide00caf5ae378104f99611bf197e896d1b53d7d7

Revision c1e94319 (diff)
Added by Mark Abraham about 4 years ago

Updated grompp cut-off and PME-Switch checks

Added a warning with PME-Switch when switching over more than 5%.
Charge-group size rlist notes/warnings now also appear when
potential modifiers are used.
Documented effect of potential-modifiers on the group scheme cut-off
treatment in mdp_opt.html.

Fixes #1179

Change-Id: Ide00caf5ae378104f99611bf197e896d1b53d7d7

History

#1 Updated by Mark Abraham about 4 years ago

  • Status changed from In Progress to Fix uploaded
  • Affected version set to 4.6.1

#2 Updated by Michael Shirts about 4 years ago

I'm still suspicious about exact cutoffs for free energy calculations, but it's on me to show that there's an issue. One of the list of things that needs to be done in the next week or two.

#3 Updated by Mark Abraham about 4 years ago

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

#4 Updated by Mark Abraham about 4 years ago

  • Status changed from Resolved to In Progress

Ongoing debate about this issue in https://gerrit.gromacs.org/2220

#5 Updated by Mark Abraham about 4 years ago

  • Target version changed from 4.6.2 to 4.6.3

#6 Updated by Mark Abraham about 4 years ago

  • Status changed from In Progress to Resolved

#7 Updated by Rossen Apostolov over 3 years ago

  • Status changed from Resolved to Closed

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