Error when extending simulation
when I try to extend on of my simulations with
mdrun -deffnm pdz_cis_NVT_disre_equi_3 -cpi pdz_cis_NVT_disre_equi_3.cpt -append
I get the following error
Count mismatch for state entry disre_rm3tav, code count is 0, file count is 13
I tried the same thing for a second simulation and get the same error.
I can extend this simulation by using tpbconv and the trr file without any errors.
All the best
Fixed reading history_t from checkpoint
The use of the wrong reading function prevented reading any checkpoint
file with distance restraints, (and probably any with orientation
restraints, too) because the stored lengths of the arrays could not be
Additionally, the way a t_state is allocated on the stack and most of
the GROMACS code base assumes structures have been allocated on the
heap (and set to zero) by snew() makes the problem worse. Noted that
this is evil and must go away some time.
#6 Updated by Mark Abraham almost 6 years ago
- Status changed from In Progress to Fix uploaded
https://gerrit.gromacs.org/2350 will permit simulations with distance restraints (and, I assume, orientation restraints) to be extended. And also permit gmxcheck to work. And all that even from earlier 4.6 checkpoint files.