Bug #1329
It is often useful to output the potential energy in the dhdl, rather than the total energy.
Description
When mdrun -rerun'ing, the kinetic energy is frequently wrong. Thus, it is preferable to print the potential energy to dhdl rather than the total energy.
instead of being a boolean, proposed change is that dhdl-print-energy, instead of being boolean, takes options 'potential', 'total', 'yes' (same as 'total') and 'no'.
The change does not require a change in the tpr (gmx_bool is an int), and no defaults are changed, thus I propose to check this in for 4.6.
A fix will be checked in soon.
Associated revisions
History
#1 Updated by Michael Shirts about 6 years ago
- Status changed from New to Fix uploaded
Fix uploaded.
#2 Updated by Michael Shirts about 6 years ago
- Target version changed from 4.6.5 to 4.6.4
#3 Updated by Mark Abraham almost 6 years ago
- Target version changed from 4.6.4 to 4.6.x
#4 Updated by Mark Abraham almost 6 years ago
- Target version changed from 4.6.x to 5.0
#5 Updated by Rossen Apostolov almost 6 years ago
fix is here: https://gerrit.gromacs.org/#/c/2815/
#6 Updated by Gerrit Code Review Bot over 5 years ago
Gerrit received a related patchset '1' for Issue #1329.
Uploader: Erik Lindahl (erik@kth.se)
Change-Id: I16828ef07c46bcfc61fe03744cbf251c00160636
Gerrit URL: https://gerrit.gromacs.org/3682
#7 Updated by Erik Lindahl over 5 years ago
- Status changed from Fix uploaded to Resolved
#8 Updated by Erik Lindahl over 5 years ago
- Status changed from Resolved to Closed
Allow printing potential energies to dhdl.xvg file
Previously, only total energies were printed out to the dhdl.xvg
file. In many cases, it is more useful to print out just
the potential energies. For example, when doing mdrun -rerun,
and comparing to output run without rerun, the velocities may not
be identical, which makes it difficult to compare the total
energies between runs when computing free energies and other
observables. dhdl-print-energy can now be 'no', 'total',
or 'potential'. The alternative 'kinetic' should generally not
be needed, since that can be done analytically in all cases.
Backwards compatible in the .tpr since gmx_bool is an int. The
old false value will be interpreted as 'no', and the 'yes' value
as 'total' energy, which will reproduce the old behavior.
Fixes #1329
Change-Id: I16828ef07c46bcfc61fe03744cbf251c00160636