Hello,
I recently used mdrun -pd while attempting to solve my problems with
angle_restraints_z
(http://lists.gromacs.org/pipermail/gmx-users/2010-January/047785.html) since
I discovered that -noddcheck is not a valid solution to the missing
interactions problems with angle restraints.
I received immediate errors with particle decomposition (mdrun -pd),
although no errors with domain decomposition (mdrun -dd).
After a couple of days of changing parameters, I discovered that mdrun
-pd requires an input .gro file in which all molecules are whole (as
the used to be written out by gromacs mdrun version 3).
My basic problem was that I had run parallel EM using domain
decomposition and then since my molecules were broken, parallel MD
using particle decomposition failed.
The solution:
grompp -f one.gro -o my.tpr
trjconv -s my.tpr -pbc mol -o two.gro
grompp -f two.gro -o my.tpr
I'm posting so that this can be found by a mailing list search for the
next time somebody runs into this as it is, as far as I can tell, an
undocumented requirement.
Chris.
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