I'm a bit confused with siesta myself. However, keep in mind that there are other files that are needed for a seemless restart. For instance, the SystemLabel.DM file is needed to restart calcualtion during the iscf steps. (See pg 60 of the manual) For good measure, you should include everything, but back up your SystemLabel.out and CLOCK files before restarting as those are obliterated. Also, I'm not entirely sure about this, you should look into the DM.MixSCF1 option (See pg 36 of the manual). But regardless, I guess it all depends on where the run stops. Sorry I can't be more help; I've been running into my fair share of problems using siesta for MD - I'm not much of an expert.

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