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

[George Rydlew]

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:

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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