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.
I recall that this is also the case for position restraints and a shuffled or
sorted run. I believe that this is a known issue and that there is no solution.
However, I can't remember where I read that I didn't find it either with a
quick search of the mailing list and the manual fo things like posre shuffle or
restraint shuffle
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