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Feature #1028

Tool to calculate fraction of native contacts during simulation

Added by bipin singh almost 7 years ago. Updated almost 7 years ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
analysis tools
Target version:
-
Difficulty:
uncategorized
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Description

Currently there is no way to calculate fraction of native contacts during the simulation in GROMACS. It would be a nice feature if one could modify the existing tools to get this feature as most of the popular MD packages contains this analysis script (Also fraction of native contacts is being widely used as reaction coordinate in protein folding/unfolding studies).
As suggested by Justin and Eric, one could modify the g_mindist code or modify the the g_hbond code to get the -sel option to work again then one would get such information with -contact option.

History

#1 Updated by Szilárd Páll almost 7 years ago

  • Target version deleted (4.5.6)

No features request for 4.x, new features have to go into 5.x.

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

  • Assignee deleted (David van der Spoel)
  • Priority changed from High to Normal

g_hbond will probable be modularized to some extent based on the new analysis framework in 5.0. I definitely don't have time for this. Priority set to normal since this is not a crucial issue.

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