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Feature #1231

single-point energies

Added by Mark Abraham almost 7 years ago. Updated over 5 years ago.

Status:
Closed
Priority:
Low
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Difficulty:
uncategorized
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Description

New users always seem to assume a zero-step MD is a single-point energy, but this is only true with unconstrained-start having the right value.

grompp should warn when the erroneous combination is used.

grompp should note in either case that mdrun -rerun should be used.

IIRC zero-step EM already does some similar output. Not sure whether that is in mdrun or not - if so, move to grompp.

Associated revisions

Revision f3c4bd6b (diff)
Added by Erik Lindahl over 5 years ago

Warn if using nsteps=0 without continuation=yes

To achieve true single-point energy evaluations for a structure
we should not constrain the initial conformation. This is
typically done by settings nsteps=0, so grompp now warns if this
is used while keeping continuation = no (the default).

Fixes #1231.

Change-Id: I4e65b66f6535da4206e7dbd5f7769a33c94ec12d

History

#1 Updated by Mark Abraham over 6 years ago

Also treat mdrun -nstep 0 the same way as .mdp setting nsteps = 0

#2 Updated by Mark Abraham over 6 years ago

  • Target version set to 4.6.4

#3 Updated by Mark Abraham over 6 years ago

  • Target version changed from 4.6.4 to 4.6.x

#4 Updated by Erik Lindahl over 5 years ago

  • Tracker changed from Bug to Feature

#5 Updated by Mark Abraham over 5 years ago

  • Target version changed from 4.6.x to 5.x

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

Gerrit received a related patchset '1' for Issue #1231.
Uploader: Erik Lindahl ()
Change-Id: I4e65b66f6535da4206e7dbd5f7769a33c94ec12d
Gerrit URL: https://gerrit.gromacs.org/3655

#7 Updated by Erik Lindahl over 5 years ago

  • Status changed from New to Resolved

#8 Updated by Erik Lindahl over 5 years ago

  • Status changed from Resolved to Closed

#9 Updated by Teemu Murtola over 5 years ago

  • Assignee changed from Mark Abraham to Erik Lindahl
  • Target version changed from 5.x to 5.0

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