[gmx-developers] incorrect distance restraints violation in energy output with checkpoints

Daniel Larsson larsson at xray.bmc.uu.se
Fri Apr 8 16:13:51 CEST 2011

The distance restraint violations stored in the energy files of my simulations have non-continuous values. The jumps occur at the point of restarts with checkpoint files. The distance restraint energies does not have large jumps at these time points and the coordinates in the xtc files do not show any large shifts.

Something perhaps missing in the checkpointing?


From mdout.mdp:

; NMR refinement stuff 
; Distance restraints type: No, Simple or Ensemble
disre                    = Simple
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting          = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed              = no
disre-fc                 = 100
disre-tau                = 0
; Output frequency for pair distances to energy file
nstdisreout              = 0
; Orientation restraints: No or Yes
orire                    = no
; Orientation restraints force constant and tau for time averaging
orire-fc                 = 0
orire-tau                = 0
orire-fitgrp             = 
; Output frequency for trace(SD) and S to energy file
nstorireout              = 100
; Dihedral angle restraints: No or Yes
dihre                    = no
dihre-fc                 = 1000

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