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

Berk Hess gmx3 at hotmail.com
Fri Jan 8 11:16:55 CET 2010


Have you actually tried increasing -rdd to the distance the maximum distance
that can occur between the two atoms in the angle restraint?


> Date: Sun, 3 Jan 2010 15:53:36 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] particle decomposition requires preliminary trjconv	-pbc mol input
> 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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