Dear all,
I have encountered noticeable differences while using the pull code with
the -shuffle -sort options in parallel, as opposed to running in serial
or in parallel without the options. Using -shuffle -sort, the dynamics
of the molecule of interest appears to be unaffected by the pulling
potential. Without the options, the molecule can be seen to be correctly
pulled in the desired direction. I'm using version 3.3.1, and this
problem is present in both single and double precision versions.
One idea is that deshuf.ndx should be modified to include the pulled
molecule reference group. A search of the mailing list archive and
manual didn't find this issue addressed. Suggestions would be
appreciated.
A representative pull.ppa file used:
verbose = no
runtype = umbrella
group_1 = NNC
reference_group = REF_MCS
reftype = com
pulldim = N N Y
k1 = 5000.0
pos1 = 0 0 0.0
and the programs are invoked with:
grompp_d -sort -shuffle -np 4
mpirun -np 4 mdrun_d -v -pi pull.ppa -pn index.ndx
Regards,
Steve Fiedler
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