Feature #1231
single-point energies
Status:
Closed
Priority:
Low
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Difficulty:
uncategorized
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
History
#1 Updated by Mark Abraham over 7 years ago
Also treat mdrun -nstep 0 the same way as .mdp setting nsteps = 0
#2 Updated by Mark Abraham over 7 years ago
- Target version set to 4.6.4
#3 Updated by Mark Abraham over 7 years ago
- Target version changed from 4.6.4 to 4.6.x
#4 Updated by Erik Lindahl over 6 years ago
- Tracker changed from Bug to Feature
#5 Updated by Mark Abraham over 6 years ago
- Target version changed from 4.6.x to 5.x
#6 Updated by Gerrit Code Review Bot over 6 years ago
Gerrit received a related patchset '1' for Issue #1231.
Uploader: Erik Lindahl (erik@kth.se)
Change-Id: I4e65b66f6535da4206e7dbd5f7769a33c94ec12d
Gerrit URL: https://gerrit.gromacs.org/3655
#7 Updated by Erik Lindahl over 6 years ago
- Status changed from New to Resolved
#8 Updated by Erik Lindahl over 6 years ago
- Status changed from Resolved to Closed
#9 Updated by Teemu Murtola over 6 years ago
- Assignee changed from Mark Abraham to Erik Lindahl
- Target version changed from 5.x to 5.0
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