[gmx-users] Problems with PBC and constraints while doing parallel runs

David spoel at xray.bmc.uu.se
Mon Nov 7 20:48:00 CET 2005

On Mon, 2005-11-07 at 19:47 +0100, George Rydlew wrote:
> Dear GROMACS users,
>   I am doing POPC membrane simulation using gromacs 3.1.4 with:
> pbc = xyz
> constraints =  hbonds
> constraint_algorithm = shake
> put in parameter file. Everything goes without any problems as long as
> I run it in serial. However any attempts to continue simulation in
> parallel causes either "inconsistent shifts" or "Shake did not
> converge in 1000 steps" errors.
> In particular when
> unconstrained_start = yes
> gen_vel =  no
> is set in md.mdp and followed by:
> grompp -f md.mdp -n popc.ndx -deshuf popc_deshuf.ndx -p popc.top -t
> popc-serial.trr -c popc-serial.gro -np 2 -shuffle -o popc-parallel.tpr
> mpirun -np 2 mdrun_mpi -deffnm popc-parallel
> mdrun crashes with "inconsistent shifts". Another way around:
The problem may be that your topology gets shuffled, but not your
coordinates. Try it without shuffle first. If that work make an inverse 
deshuf.ndx file from the original deshuf.ndx and apply that to your
original trr (last frame only will suffice):
trjconv -f popc-serial.trr -b XXX -n reshuf.ndx -o reshuffled.trr
and feed that trr file to grompp.

> trjconv -f popc-serial.trr -o par-in.gro -s popc-serial.tpr -n
> popc.ndx -b 25480 -e 25480
> grompp -f md.mdp -n popc.ndx -deshuf popc_deshuf.ndx -p popc.top -c
> par-in.gro -np 2 -shuffle -o popc-parallel.tpr
> mpirun -np 2 mdrun_mpi -deffnm popc-parallel
> causes "Shake did not converge in 1000 steps" and simulation crash
> within few subsequent steps (here md.mdp was also altered to perform
> unconstrained run and preserve velocities). I tried to solve this by
> setting GMXFULLPBC to 1 but to no avail in both cases.
> Now, I managed to continue simulation in gromacs 3.2.1 by extracting
> last frame from the trajectory (second approach from the above). Doing
> grompp with "-t popc-serial.trr" was causing "inconsistent shifts"
> also in this version. Anyway, I don't like that solution, as it
> requires changing of gromacs version in the middle of simulation and,
> as far as I understood, does not perform accurate restart due to
> precision of velocities in .gro file.
> Thanks in advance for any clue on what is the reason for such behavior
> and possible solutions.
> Sincerely Yours,
>   G. Rydlew
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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