[gmx-users] particle decomposition requires preliminary trjconv -pbc mol input

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Jan 3 21:53:36 CET 2010


I recently used mdrun -pd while attempting to solve my problems with  
(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.


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