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This was a stupid mistake on our part. While we were testing the software, and the tutorial instructions, the files were not on a CD yet -- they were on a hard drive. When a user starts an averaging calculation with MD, the .CSV file is opened for writing in the default directory -- i.e., the one that the .SNP file is in. This is fine on a hard drive, but is doomed to failure when that directory is on a CD.
The simplest work-around is to copy the .HIN and .SNP files from the CD to your hard drive for a dynamics playback that you want to calculate averages with. If you just want to play back a dynamics run without calculating averages, of course, this is not necessary.
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